Transformations of breast cancer transcriptional cohorts

M Hallett

21/07/2020

Simpson’s Paradox

Simpson’s paradox: The phenomenon where a trend appears in several different groups of data but disappears or reverses when these groups are combined.

Suppose here we asked a group of people how much they paid for their car and how satified they are with it.
When we are not aware that the points (samples, people, objects) belong to two distinct groups (eg poor vs rich, tumor vs normal, patients vs healthy etc) the data suggests an upward trend.
However if we were told that the blue points are low income people and red are high income, our interpretation might change.
How would interpret these plots?
Your challenge is to figure out how this relates to today’s lecture.

Outline for today

Today we investigate the Transform in the the Transform \(\rightarrow\) Visualize \(\rightarrow\) Model cycle.

We will return to our \({\tt tcga\_brca}\) breast cancer transcriptomics dataset.
Transformations select specific subsets of the data for visualization and modelling.

What are we fighting for?

First let’s ask why do we want to do data science on BC transcriptomes, or any other dataset for that matter? What are our goals? What motivates the study?

Old Protest Song

Ok, it’s certainly not warfare but the analysis of datasets can quickly result in a quagmire that takes months or years to complete.
It’s important to go into the analysis with a set of questions that are as clear and well-defined as posible. Not perhaps as precise as clinical trials, but awareness of the design, power and goals of the experiment really help avoid long protracted struggles with the data and false findings.

Common goals in cancer informatics

Basic science, for sure.
Better underestanding of the molecular basis of BC. Eg which genes, pathways and processes are at play in each subtype of the disease. This might lead to new therapies or therapeutic avenues.
Discover ways to intervene clinically. What is the clinical end-point of the study?
Clinical endpoints are distinct measurements or analyses of disease characteristics observed in a research study or a clinical trial that reflect the effect of a therapeutic intervention.

Examples of research projects for different clinical endpoints

Disease Marker Find a gene(s) that indicates a woman (in the population) is at risk of developing breast cancer.
Screening Build image analysis technology to identify with high accuracy very small tumors in the mammary gland.
Diagnosis Find a gene(s) or gene products that accurately confirm that a woman does or does not have breast cancer (eg analogous to a pregnancy test).
Classification Given that a woman has been diagnosed with BC, find a gene(s) or gene products that classify her tumor into the correct subtype.
Prognosis Given that a woman has been diagnosed with a specific type of BC, predict how long she will live disease-free post-initial treatment/surgery.
Benefit from Therapy Given the characteristics of a woman’s tumor, predict whether she will or will not benefit from a specific therapy.
Monitoring Find a gene(s) or gene products that faithfully report if a new tumor (micrometastasis) has appeared in a woman post-treatment.

Clinical Validity and Utility

Whatever the endpoint is, ideally the endpoint has these two properties.
Clinical utility means that the result of your research can be used by clinicians to change their decision making in precise ways.
Clinicial validity means that the result of your research generalizes to the intended population, and remains able to function with sufficient efficacy.

Bottomline here

Bio-data is inherently very noisey.
Technical noise due to inaccurate measurements and bias in the measurements.
Biological noise due to natural variability between patients (eg small genetic differences), cells (eg cell cycle fluctuations) and diferences due to lifestyle etc.
When starting out your analysis, it is wise to search for a core homogenous subgroup. It might be easier to solve the problem (eg find the gene or gene products for your endpoint) in this core group first, and then expand your analysis out to the larger cohort.
I will give some examples of transformations now.

Initialize our session

We are going to focus on a package called \({\tt dplyr}\) today. It’s also part of the \({\tt tidyverse}\).
If \({\tt ggplot2}\) is the grammar of plots, \({\tt dplyr}\) is the grammer of data transformation.

library(tidyverse)
load("~/data/GDC/TCGA_BRCA/small_brca.Rdata")   # load the BC dataset
#View(small_brca)                # handy to have that open for exploration

Note the class of the different attributes

There are three classes here: \({\tt character (chr)}\), \({\tt lgl (logical)}\) and \({\tt dbl (double)}\). Note that \({\tt double}\) is the same as \({\tt numeric}\). Historical anomaly.

small_brca               
## # A tibble: 1,215 x 79
##    id    tss   participant barcode bcr_patient_uuid form_completion…
##    <chr> <chr> <chr>       <chr>   <chr>            <chr>           
##  1 TCGA… E9    A1NF        TCGA-E… a8b1f6e7-2bcf-4… 2011-6-23       
##  2 TCGA… D8    A27M        TCGA-D… ae65baeb-6b78-4… 2011-7-17       
##  3 TCGA… BH    A0GZ        TCGA-B… 27dfb9d4-3a2c-4… 2010-11-10      
##  4 TCGA… BH    A18V        TCGA-B… 6b960b58-28e1-4… 2011-7-2        
##  5 TCGA… A7    A13G        TCGA-A… 6cd9baf5-bbe0-4… 2011-5-16       
##  6 TCGA… C8    A275        TCGA-C… ce887e90-0660-4… 2011-7-21       
##  7 TCGA… AN    A0XS        TCGA-A… 95e949d3-b1f3-4… 2011-3-28       
##  8 TCGA… OL    A5RW        TCGA-O… A82D0A57-4383-4… 2013-5-16       
##  9 TCGA… OL    A5RX        TCGA-O… 43C0BEC6-6FAC-4… 2013-5-16       
## 10 TCGA… E9    A1RD        TCGA-E… 5fe3c51f-65e2-4… 2011-7-28       
## # … with 1,205 more rows, and 73 more variables: birth_days_to <chr>,
## #   gender <chr>, menopause_status <chr>, race <chr>, ethnicity <chr>,
## #   tumor_status <chr>, vital_status <chr>, death_days_to <chr>,
## #   histologic_diagnosis_other <chr>, initial_pathologic_dx_year <chr>,
## #   age_at_diagnosis <chr>, micromet_detection_by_ihc <chr>,
## #   lymph_nodes_examined_count <chr>, ajcc_pathologic_tumor_stage <chr>,
## #   er_status_by_ihc <chr>, er_status_ihc_Percent_Positive <chr>,
## #   pr_status_by_ihc <chr>, pr_status_ihc_percent_positive <chr>,
## #   her2_fish_status <chr>, her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

There are other classes not used here. We will see \({\tt fctr (factors)}\) later.

\({\tt dplyr}\) cheat sheet (part 1)

variables are columns; observations are rows.

\({\tt dplyr}\) cheat sheet (part 2)

Available here
Mounted R cheat sheets make great gifts for Bioinformaticians!

Filtering observations

Remember: variables are columns; observations are rows. Sometimes you want to analyze just a subset of all your observations (rows; samples). Before visualization, you need to remove unwanted rows. And that’s why the \({\tt filter()}\) functions exist.
For example, let’s remove the morphologically normal samples from the analysis.

Filtering out normal samples

(tumor_brca <- filter(small_brca, tumor==TRUE))               
## # A tibble: 1,102 x 79
##    id    tss   participant barcode bcr_patient_uuid form_completion…
##    <chr> <chr> <chr>       <chr>   <chr>            <chr>           
##  1 TCGA… E9    A1NF        TCGA-E… a8b1f6e7-2bcf-4… 2011-6-23       
##  2 TCGA… D8    A27M        TCGA-D… ae65baeb-6b78-4… 2011-7-17       
##  3 TCGA… BH    A0GZ        TCGA-B… 27dfb9d4-3a2c-4… 2010-11-10      
##  4 TCGA… BH    A18V        TCGA-B… 6b960b58-28e1-4… 2011-7-2        
##  5 TCGA… A7    A13G        TCGA-A… 6cd9baf5-bbe0-4… 2011-5-16       
##  6 TCGA… C8    A275        TCGA-C… ce887e90-0660-4… 2011-7-21       
##  7 TCGA… AN    A0XS        TCGA-A… 95e949d3-b1f3-4… 2011-3-28       
##  8 TCGA… OL    A5RW        TCGA-O… A82D0A57-4383-4… 2013-5-16       
##  9 TCGA… OL    A5RX        TCGA-O… 43C0BEC6-6FAC-4… 2013-5-16       
## 10 TCGA… E9    A1RD        TCGA-E… 5fe3c51f-65e2-4… 2011-7-28       
## # … with 1,092 more rows, and 73 more variables: birth_days_to <chr>,
## #   gender <chr>, menopause_status <chr>, race <chr>, ethnicity <chr>,
## #   tumor_status <chr>, vital_status <chr>, death_days_to <chr>,
## #   histologic_diagnosis_other <chr>, initial_pathologic_dx_year <chr>,
## #   age_at_diagnosis <chr>, micromet_detection_by_ihc <chr>,
## #   lymph_nodes_examined_count <chr>, ajcc_pathologic_tumor_stage <chr>,
## #   er_status_by_ihc <chr>, er_status_ihc_Percent_Positive <chr>,
## #   pr_status_by_ihc <chr>, pr_status_ihc_percent_positive <chr>,
## #   her2_fish_status <chr>, her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

Let’s make sure that worked

Filtering out samples with unknown or ill-defined TNM stage

Recall from Lecture 02 our disucssion of TNM staging.

unique(tumor_brca$ajcc_pathologic_tumor_stage)
##  [1] "Stage IIA"       "Stage IA"        "Stage IIB"       "Stage IIIA"     
##  [5] "Stage IB"        "Stage I"         "Stage IIIC"      "Stage IV"       
##  [9] "[Discrepancy]"   "Stage II"        "Stage IIIB"      "[Not Available]"
## [13] "Stage X"         NA                "Stage III"

\({\tt unique()}\) returns the distinct (or unique) objects observed in a (long) vector of objects. Try removing the \({\tt unique()}\) call from above and see what happens.
There are four (of 15) types of objects that I would like to remove from the analysis to begin with: 9, 12, 13, 14.
Note the NA for #14. Not that same as the character “[Not Available]” #12 (but both must go!).

Filtering by TNM stage

(tnm_tumor_brca <- filter(tumor_brca, !( (is.na(ajcc_pathologic_tumor_stage) |
                                         (ajcc_pathologic_tumor_stage == "[Discrepancy]") |
                                         (ajcc_pathologic_tumor_stage == "[Not Available]") |
                                         (ajcc_pathologic_tumor_stage == "Stage X") ) )   ) )
## # A tibble: 1,078 x 79
##    id    tss   participant barcode bcr_patient_uuid form_completion…
##    <chr> <chr> <chr>       <chr>   <chr>            <chr>           
##  1 TCGA… E9    A1NF        TCGA-E… a8b1f6e7-2bcf-4… 2011-6-23       
##  2 TCGA… D8    A27M        TCGA-D… ae65baeb-6b78-4… 2011-7-17       
##  3 TCGA… BH    A0GZ        TCGA-B… 27dfb9d4-3a2c-4… 2010-11-10      
##  4 TCGA… BH    A18V        TCGA-B… 6b960b58-28e1-4… 2011-7-2        
##  5 TCGA… A7    A13G        TCGA-A… 6cd9baf5-bbe0-4… 2011-5-16       
##  6 TCGA… C8    A275        TCGA-C… ce887e90-0660-4… 2011-7-21       
##  7 TCGA… AN    A0XS        TCGA-A… 95e949d3-b1f3-4… 2011-3-28       
##  8 TCGA… OL    A5RW        TCGA-O… A82D0A57-4383-4… 2013-5-16       
##  9 TCGA… OL    A5RX        TCGA-O… 43C0BEC6-6FAC-4… 2013-5-16       
## 10 TCGA… E9    A1RD        TCGA-E… 5fe3c51f-65e2-4… 2011-7-28       
## # … with 1,068 more rows, and 73 more variables: birth_days_to <chr>,
## #   gender <chr>, menopause_status <chr>, race <chr>, ethnicity <chr>,
## #   tumor_status <chr>, vital_status <chr>, death_days_to <chr>,
## #   histologic_diagnosis_other <chr>, initial_pathologic_dx_year <chr>,
## #   age_at_diagnosis <chr>, micromet_detection_by_ihc <chr>,
## #   lymph_nodes_examined_count <chr>, ajcc_pathologic_tumor_stage <chr>,
## #   er_status_by_ihc <chr>, er_status_ihc_Percent_Positive <chr>,
## #   pr_status_by_ihc <chr>, pr_status_ihc_percent_positive <chr>,
## #   her2_fish_status <chr>, her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

Note the logical expression using the \({\tt !~(not)}\) operator and the \({\tt |~(or)}\) operator.
This also works (try to understand why \({\tt ? ~ grepl()}\) ):

filter(tumor_brca, grepl(“Stage”, ajcc_pathologic_tumor_stage))

Arranging the observations

Sometimes we don’t want to filter out observations but simply arrange them in a more informative manner.
Our goal here is to sort first by TNM stage, and then according to how many days they survived since diagnosis.

sorted_tnm_tumor_brca <- arrange(tnm_tumor_brca, ajcc_pathologic_tumor_stage, death_days_to)
head(sorted_tnm_tumor_brca)
## # A tibble: 6 x 79
##   id    tss   participant barcode bcr_patient_uuid form_completion…
##   <chr> <chr> <chr>       <chr>   <chr>            <chr>           
## 1 TCGA… A1    A0SB        TCGA-A… 0045349c-69d9-4… 2011-6-30       
## 2 TCGA… A8    A08A        TCGA-A… 7fe4670d-4626-4… 2011-5-27       
## 3 TCGA… E2    A156        TCGA-E… f05d314c-5ec5-4… 2011-4-7        
## 4 TCGA… A8    A095        TCGA-A… 29df128d-ace2-4… 2011-5-27       
## 5 TCGA… AR    A255        TCGA-A… e8f3cc64-5e15-4… 2011-8-31       
## 6 TCGA… AR    A24S        TCGA-A… 074e8b06-3929-4… 2011-8-30       
## # … with 73 more variables: birth_days_to <chr>, gender <chr>,
## #   menopause_status <chr>, race <chr>, ethnicity <chr>, tumor_status <chr>,
## #   vital_status <chr>, death_days_to <chr>, histologic_diagnosis_other <chr>,
## #   initial_pathologic_dx_year <chr>, age_at_diagnosis <chr>,
## #   micromet_detection_by_ihc <chr>, lymph_nodes_examined_count <chr>,
## #   ajcc_pathologic_tumor_stage <chr>, er_status_by_ihc <chr>,
## #   er_status_ihc_Percent_Positive <chr>, pr_status_by_ihc <chr>,
## #   pr_status_ihc_percent_positive <chr>, her2_fish_status <chr>,
## #   her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

Arranging the observations by TNM and survival time

tail(sorted_tnm_tumor_brca)
## # A tibble: 6 x 79
##   id    tss   participant barcode bcr_patient_uuid form_completion…
##   <chr> <chr> <chr>       <chr>   <chr>            <chr>           
## 1 TCGA… A2    A0SW        TCGA-A… 991e1427-3c01-4… 2010-11-8       
## 2 TCGA… A2    A0T2        TCGA-A… 128d198e-9b22-4… 2010-11-12      
## 3 TCGA… B6    A0I9        TCGA-B… 44954053-0b93-4… 2010-11-2       
## 4 TCGA… B6    A0IB        TCGA-B… 157ec9e0-ca6e-4… 2010-11-2       
## 5 TCGA… BH    A18J        TCGA-B… cc074b7f-d3b2-4… 2011-6-8        
## 6 TCGA… A2    A0SV        TCGA-A… ad01259b-d858-4… 2010-11-15      
## # … with 73 more variables: birth_days_to <chr>, gender <chr>,
## #   menopause_status <chr>, race <chr>, ethnicity <chr>, tumor_status <chr>,
## #   vital_status <chr>, death_days_to <chr>, histologic_diagnosis_other <chr>,
## #   initial_pathologic_dx_year <chr>, age_at_diagnosis <chr>,
## #   micromet_detection_by_ihc <chr>, lymph_nodes_examined_count <chr>,
## #   ajcc_pathologic_tumor_stage <chr>, er_status_by_ihc <chr>,
## #   er_status_ihc_Percent_Positive <chr>, pr_status_by_ihc <chr>,
## #   pr_status_ihc_percent_positive <chr>, her2_fish_status <chr>,
## #   her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

What happened here?
Hint: What is the type of \({\tt deaths\_days\_to}\)?
How do we fix this?

Converting the type of a variable (column)

Currently, \({\tt death\_days\_to}\) has type \({\tt character}\).
lexicographical ordering: “a” < “ab” < “b”
“1” < “12” < “2”
1 < 2 < 12

tail(sorted_tnm_tumor_brca[, c( "ajcc_pathologic_tumor_stage", "vital_status", "death_days_to")])
## # A tibble: 6 x 3
##   ajcc_pathologic_tumor_stage vital_status death_days_to
##   <chr>                       <chr>        <chr>        
## 1 Stage IV                    Dead         1365         
## 2 Stage IV                    Dead         255          
## 3 Stage IV                    Dead         362          
## 4 Stage IV                    Dead         3941         
## 5 Stage IV                    Dead         612          
## 6 Stage IV                    Dead         825

sorted_tnm_tumor_brca$death_days_to <- as.numeric( sorted_tnm_tumor_brca$death_days_to )
## Warning: NAs introduced by coercion

Converting the type of a variable (column)

tail(sorted_tnm_tumor_brca[, c( "ajcc_pathologic_tumor_stage", "vital_status", "death_days_to")])
## # A tibble: 6 x 3
##   ajcc_pathologic_tumor_stage vital_status death_days_to
##   <chr>                       <chr>                <dbl>
## 1 Stage IV                    Dead                  1365
## 2 Stage IV                    Dead                   255
## 3 Stage IV                    Dead                   362
## 4 Stage IV                    Dead                  3941
## 5 Stage IV                    Dead                   612
## 6 Stage IV                    Dead                   825

Note that the \({\tt chr}\) is now a \({\tt double~(dbl)}\) (a real number).
Note also that we haven’t re-sorted yet… That’s next…

Converting the type of a variable (column)

final_brca <- arrange(sorted_tnm_tumor_brca, ajcc_pathologic_tumor_stage, death_days_to)
final_brca[1058:1068, c( "ajcc_pathologic_tumor_stage",  "death_days_to")]
## # A tibble: 11 x 2
##    ajcc_pathologic_tumor_stage death_days_to
##    <chr>                               <dbl>
##  1 Stage IIIC                             NA
##  2 Stage IV                              116
##  3 Stage IV                              255
##  4 Stage IV                              362
##  5 Stage IV                              612
##  6 Stage IV                              825
##  7 Stage IV                             1034
##  8 Stage IV                             1127
##  9 Stage IV                             1365
## 10 Stage IV                             3941
## 11 Stage IV                               NA

???

But TNM stage (variable \({\tt ajcc\_pathologic\_tumor\_stage}\)) is also a \({\tt character}\); why did it sort correctly?

final_brca$ajcc_pathologic_tumor_stage
##    [1] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##    [6] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [11] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [16] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [21] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [26] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [31] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [36] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [41] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [46] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [51] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [56] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [61] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [66] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [71] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [76] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [81] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage I"   
##   [86] "Stage I"    "Stage I"    "Stage I"    "Stage I"    "Stage IA"  
##   [91] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##   [96] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [101] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [106] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [111] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [116] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [121] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [126] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [131] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [136] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [141] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [146] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [151] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [156] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [161] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [166] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [171] "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"   "Stage IA"  
##  [176] "Stage IA"   "Stage IB"   "Stage IB"   "Stage IB"   "Stage IB"  
##  [181] "Stage IB"   "Stage IB"   "Stage II"   "Stage II"   "Stage II"  
##  [186] "Stage II"   "Stage II"   "Stage II"   "Stage IIA"  "Stage IIA" 
##  [191] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [196] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [201] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [206] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [211] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [216] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [221] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [226] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [231] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [236] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [241] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [246] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [251] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [256] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [261] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [266] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [271] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [276] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [281] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [286] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [291] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [296] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [301] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [306] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [311] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [316] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [321] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [326] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [331] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [336] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [341] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [346] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [351] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [356] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [361] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [366] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [371] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [376] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [381] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [386] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [391] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [396] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [401] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [406] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [411] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [416] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [421] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [426] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [431] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [436] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [441] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [446] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [451] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [456] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [461] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [466] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [471] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [476] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [481] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [486] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [491] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [496] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [501] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [506] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [511] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [516] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [521] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [526] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [531] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [536] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [541] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [546] "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA"  "Stage IIA" 
##  [551] "Stage IIA"  "Stage IIA"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [556] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [561] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [566] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [571] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [576] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [581] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [586] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [591] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [596] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [601] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [606] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [611] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [616] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [621] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [626] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [631] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [636] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [641] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [646] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [651] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [656] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [661] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [666] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [671] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [676] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [681] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [686] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [691] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [696] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [701] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [706] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [711] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [716] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [721] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [726] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [731] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [736] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [741] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [746] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [751] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [756] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [761] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [766] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [771] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [776] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [781] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [786] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [791] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [796] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [801] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB" 
##  [806] "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage IIB"  "Stage III" 
##  [811] "Stage III"  "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [816] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [821] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [826] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [831] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [836] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [841] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [846] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [851] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [856] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [861] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [866] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [871] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [876] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [881] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [886] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [891] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [896] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [901] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [906] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [911] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [916] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [921] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [926] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [931] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [936] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [941] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [946] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [951] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [956] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [961] "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA" "Stage IIIA"
##  [966] "Stage IIIA" "Stage IIIA" "Stage IIIB" "Stage IIIB" "Stage IIIB"
##  [971] "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIB"
##  [976] "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIB"
##  [981] "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIB"
##  [986] "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIB"
##  [991] "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIB" "Stage IIIC"
##  [996] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1001] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1006] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1011] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1016] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1021] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1026] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1031] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1036] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1041] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1046] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1051] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IIIC"
## [1056] "Stage IIIC" "Stage IIIC" "Stage IIIC" "Stage IV"   "Stage IV"  
## [1061] "Stage IV"   "Stage IV"   "Stage IV"   "Stage IV"   "Stage IV"  
## [1066] "Stage IV"   "Stage IV"   "Stage IV"   "Stage IV"   "Stage IV"  
## [1071] "Stage IV"   "Stage IV"   "Stage IV"   "Stage IV"   "Stage IV"  
## [1076] "Stage IV"   "Stage IV"   "Stage IV"

Selecting variables (columns)

Sometimes after you have downloaded data and wrangled it into a \({\tt tibble}\), there are some variables (columns) that you are perhaps not interested in.
The \({\tt select()}\) function is designed to easily pick out variables you want from those you don’t.

final_brca
## # A tibble: 1,078 x 79
##    id    tss   participant barcode bcr_patient_uuid form_completion…
##    <chr> <chr> <chr>       <chr>   <chr>            <chr>           
##  1 TCGA… BH    A1FG        TCGA-B… d4e7426c-9739-4… 2011-9-8        
##  2 TCGA… BH    A18P        TCGA-B… 557cb0a3-6f1b-4… 2011-6-22       
##  3 TCGA… BH    A1FD        TCGA-B… 3c8b5af9-c34d-4… 2011-9-8        
##  4 TCGA… BH    A1EU        TCGA-B… a1093598-d3a8-4… 2011-9-7        
##  5 TCGA… AO    A03U        TCGA-A… 0685edd2-ce1c-4… 2011-1-9        
##  6 TCGA… GM    A2D9        TCGA-G… 1133B8A9-6B11-4… 2011-9-28       
##  7 TCGA… BH    A18S        TCGA-B… 433427a1-bacf-4… 2011-7-2        
##  8 TCGA… BH    A1ET        TCGA-B… 8986a141-eae7-4… 2011-9-7        
##  9 TCGA… BH    A18K        TCGA-B… 50619f8c-10aa-4… 2011-6-9        
## 10 TCGA… B6    A0X0        TCGA-B… 1e68e760-a4cf-4… 2011-3-15       
## # … with 1,068 more rows, and 73 more variables: birth_days_to <chr>,
## #   gender <chr>, menopause_status <chr>, race <chr>, ethnicity <chr>,
## #   tumor_status <chr>, vital_status <chr>, death_days_to <dbl>,
## #   histologic_diagnosis_other <chr>, initial_pathologic_dx_year <chr>,
## #   age_at_diagnosis <chr>, micromet_detection_by_ihc <chr>,
## #   lymph_nodes_examined_count <chr>, ajcc_pathologic_tumor_stage <chr>,
## #   er_status_by_ihc <chr>, er_status_ihc_Percent_Positive <chr>,
## #   pr_status_by_ihc <chr>, pr_status_ihc_percent_positive <chr>,
## #   her2_fish_status <chr>, her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

Selecting variables (columns)

(mini_brca <- select(final_brca, participant, birth_days_to, menopause_status, race, ethnicity))
## # A tibble: 1,078 x 5
##    participant birth_days_to menopause_status race  ethnicity             
##    <chr>       <chr>         <chr>            <chr> <chr>                 
##  1 A1FG        -32295        Post             WHITE NOT HISPANIC OR LATINO
##  2 A18P        -22222        Not Available    WHITE [Not Available]       
##  3 A1FD        -24940        Post             WHITE NOT HISPANIC OR LATINO
##  4 A1EU        -30339        Post             WHITE NOT HISPANIC OR LATINO
##  5 A03U        -11354        Pre              WHITE NOT HISPANIC OR LATINO
##  6 A2D9        -25490        Post             WHITE NOT HISPANIC OR LATINO
##  7 A18S        -28974        Post             WHITE NOT HISPANIC OR LATINO
##  8 A1ET        -20425        Not Available    WHITE NOT HISPANIC OR LATINO
##  9 A18K        -16824        Not Available    WHITE NOT HISPANIC OR LATINO
## 10 A0X0        -19802        Indeterminate    WHITE NOT HISPANIC OR LATINO
## # … with 1,068 more rows

But suppose we wanted to retain many columns (not just a few). Wearisome to type all of the columns into the \({\tt select()}\) call.

Selecting many variables with the colon operator

(mini_brca <- select(final_brca, participant, ANLN:TMEM45B ))
## # A tibble: 1,078 x 51
##    participant  ANLN FOXC1  CDH3 FGFR4 UBE2T NDC80   PGR BIRC5  ORC6   ESR1
##    <chr>       <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>  <dbl>
##  1 A1FG          816   436   542   187   384   475 10737  1795   425 102256
##  2 A18P         4099   276  1145 12773  1059   677    98  1867   222   4550
##  3 A1FD         2762   265  4416   913  1409   686 29929  4622   597  58483
##  4 A1EU          415   611   638    55   194   133 35489   323    72  75875
##  5 A03U          914  3998  9772    68   221   309   125   679   140    475
##  6 A2D9          850   405  2725  1878   505   365   756   308    75  40483
##  7 A18S          532   172   128  1577   570   170  8338   498   134  57101
##  8 A1ET          336   617   692   744   159   141 19071   411    83  73208
##  9 A18K         2541   351  1509   835  1636   610  3397  1849   205  18863
## 10 A0X0          629   226  3504   301  1054   579 15244  1370   198  23790
## # … with 1,068 more rows, and 40 more variables: PHGDH <dbl>, PTTG1 <dbl>,
## #   MELK <dbl>, NAT1 <dbl>, CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>,
## #   EXO1 <dbl>, UBE2C <dbl>, TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>,
## #   CDC6 <dbl>, MMP11 <dbl>, MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>,
## #   BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>, CDC20 <dbl>, CENPF <dbl>, MIA <dbl>,
## #   KRT17 <dbl>, FOXA1 <dbl>, ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>,
## #   CEP55 <dbl>, SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>,
## #   NUF2 <dbl>, EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

\({\tt x:y}\) selects all variables between \(x\) and \(y\) inclusive.

Removing variables with the minus operator

(mini_brca <- select(final_brca,  -c(id, tss, barcode:birth_days_to) ))
## # A tibble: 1,078 x 73
##    participant gender menopause_status race  ethnicity tumor_status vital_status
##    <chr>       <chr>  <chr>            <chr> <chr>     <chr>        <chr>       
##  1 A1FG        FEMALE Post             WHITE NOT HISP… [Not Availa… Dead        
##  2 A18P        FEMALE Not Available    WHITE [Not Ava… WITH TUMOR   Dead        
##  3 A1FD        FEMALE Post             WHITE NOT HISP… WITH TUMOR   Dead        
##  4 A1EU        FEMALE Post             WHITE NOT HISP… TUMOR FREE   Dead        
##  5 A03U        FEMALE Pre              WHITE NOT HISP… TUMOR FREE   Dead        
##  6 A2D9        FEMALE Post             WHITE NOT HISP… WITH TUMOR   Dead        
##  7 A18S        FEMALE Post             WHITE NOT HISP… TUMOR FREE   Dead        
##  8 A1ET        FEMALE Not Available    WHITE NOT HISP… TUMOR FREE   Dead        
##  9 A18K        FEMALE Not Available    WHITE NOT HISP… WITH TUMOR   Dead        
## 10 A0X0        FEMALE Indeterminate    WHITE NOT HISP… [Not Availa… Dead        
## # … with 1,068 more rows, and 66 more variables: death_days_to <dbl>,
## #   histologic_diagnosis_other <chr>, initial_pathologic_dx_year <chr>,
## #   age_at_diagnosis <chr>, micromet_detection_by_ihc <chr>,
## #   lymph_nodes_examined_count <chr>, ajcc_pathologic_tumor_stage <chr>,
## #   er_status_by_ihc <chr>, er_status_ihc_Percent_Positive <chr>,
## #   pr_status_by_ihc <chr>, pr_status_ihc_percent_positive <chr>,
## #   her2_fish_status <chr>, her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

\({\tt -}\) removes all variables between \(x\) and \(y\) inclusive.

Re-ordering variables

Sometimes you don’t want to remove variables but just highlight certain variables you look at more often.

(hilite_brca <- select(final_brca, participant, ajcc_pathologic_tumor_stage, vital_status, death_days_to, everything() ))
## # A tibble: 1,078 x 79
##    participant ajcc_pathologic… vital_status death_days_to id    tss   barcode
##    <chr>       <chr>            <chr>                <dbl> <chr> <chr> <chr>  
##  1 A1FG        Stage I          Dead                   577 TCGA… BH    TCGA-B…
##  2 A18P        Stage I          Dead                   921 TCGA… BH    TCGA-B…
##  3 A1FD        Stage I          Dead                  1009 TCGA… BH    TCGA-B…
##  4 A1EU        Stage I          Dead                  1286 TCGA… BH    TCGA-B…
##  5 A03U        Stage I          Dead                  1793 TCGA… AO    TCGA-A…
##  6 A2D9        Stage I          Dead                  1812 TCGA… GM    TCGA-G…
##  7 A18S        Stage I          Dead                  2009 TCGA… BH    TCGA-B…
##  8 A1ET        Stage I          Dead                  2520 TCGA… BH    TCGA-B…
##  9 A18K        Stage I          Dead                  2763 TCGA… BH    TCGA-B…
## 10 A0X0        Stage I          Dead                  3945 TCGA… B6    TCGA-B…
## # … with 1,068 more rows, and 72 more variables: bcr_patient_uuid <chr>,
## #   form_completion_date <chr>, birth_days_to <chr>, gender <chr>,
## #   menopause_status <chr>, race <chr>, ethnicity <chr>, tumor_status <chr>,
## #   histologic_diagnosis_other <chr>, initial_pathologic_dx_year <chr>,
## #   age_at_diagnosis <chr>, micromet_detection_by_ihc <chr>,
## #   lymph_nodes_examined_count <chr>, er_status_by_ihc <chr>,
## #   er_status_ihc_Percent_Positive <chr>, pr_status_by_ihc <chr>,
## #   pr_status_ihc_percent_positive <chr>, her2_fish_status <chr>,
## #   her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

Renaming variables

(simple_brca <- rename(hilite_brca,  stage = ajcc_pathologic_tumor_stage ))
## # A tibble: 1,078 x 79
##    participant stage vital_status death_days_to id    tss   barcode
##    <chr>       <chr> <chr>                <dbl> <chr> <chr> <chr>  
##  1 A1FG        Stag… Dead                   577 TCGA… BH    TCGA-B…
##  2 A18P        Stag… Dead                   921 TCGA… BH    TCGA-B…
##  3 A1FD        Stag… Dead                  1009 TCGA… BH    TCGA-B…
##  4 A1EU        Stag… Dead                  1286 TCGA… BH    TCGA-B…
##  5 A03U        Stag… Dead                  1793 TCGA… AO    TCGA-A…
##  6 A2D9        Stag… Dead                  1812 TCGA… GM    TCGA-G…
##  7 A18S        Stag… Dead                  2009 TCGA… BH    TCGA-B…
##  8 A1ET        Stag… Dead                  2520 TCGA… BH    TCGA-B…
##  9 A18K        Stag… Dead                  2763 TCGA… BH    TCGA-B…
## 10 A0X0        Stag… Dead                  3945 TCGA… B6    TCGA-B…
## # … with 1,068 more rows, and 72 more variables: bcr_patient_uuid <chr>,
## #   form_completion_date <chr>, birth_days_to <chr>, gender <chr>,
## #   menopause_status <chr>, race <chr>, ethnicity <chr>, tumor_status <chr>,
## #   histologic_diagnosis_other <chr>, initial_pathologic_dx_year <chr>,
## #   age_at_diagnosis <chr>, micromet_detection_by_ihc <chr>,
## #   lymph_nodes_examined_count <chr>, er_status_by_ihc <chr>,
## #   er_status_ihc_Percent_Positive <chr>, pr_status_by_ihc <chr>,
## #   pr_status_ihc_percent_positive <chr>, her2_fish_status <chr>,
## #   her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

Grouping by variables and summarizing

Suppose we ask the question: For each stage of the disease, what is the mean number of days patients survived before passing away?

reordered_brca <- group_by(simple_brca,  stage, vital_status )
print(reordered_brca[8:30, 1:4])
## # A tibble: 23 x 4
## # Groups:   stage, vital_status [2]
##    participant stage   vital_status death_days_to
##    <chr>       <chr>   <chr>                <dbl>
##  1 A1ET        Stage I Dead                  2520
##  2 A18K        Stage I Dead                  2763
##  3 A0X0        Stage I Dead                  3945
##  4 A209        Stage I Dead                  3959
##  5 A0SB        Stage I Alive                   NA
##  6 A08A        Stage I Alive                   NA
##  7 A156        Stage I Alive                   NA
##  8 A095        Stage I Alive                   NA
##  9 A255        Stage I Alive                   NA
## 10 A24S        Stage I Alive                   NA
## # … with 13 more rows

Grouping by variables and summarizing

Suppose we ask the question: For each stage of the disease, what is the mean number of days patients survived before passing away?

(answer <- summarize(reordered_brca, mean_survive = mean(death_days_to),
                          st_dev = sd(death_days_to),
                          n = n()  # this counts the number in each group
                     ))
## `summarise()` regrouping output by 'stage' (override with `.groups` argument)
## # A tibble: 20 x 5
## # Groups:   stage [11]
##    stage      vital_status mean_survive st_dev     n
##    <chr>      <chr>               <dbl>  <dbl> <int>
##  1 Stage I    Alive                 NA     NA     78
##  2 Stage I    Dead                2054   1149.    11
##  3 Stage IA   Alive                 NA     NA     85
##  4 Stage IA   Dead                 992.   985.     2
##  5 Stage IB   Alive                 NA     NA      6
##  6 Stage II   Alive                 NA     NA      6
##  7 Stage IIA  Alive                 NA     NA    340
##  8 Stage IIA  Dead                1672.   975.    24
##  9 Stage IIB  Alive                 NA     NA    237
## 10 Stage IIB  Dead                1954.  1207.    20
## 11 Stage III  Alive                 NA     NA      1
## 12 Stage III  Dead                 616     NA      1
## 13 Stage IIIA Alive                 NA     NA    138
## 14 Stage IIIA Dead                1331.  1011.    18
## 15 Stage IIIB Alive                 NA     NA     22
## 16 Stage IIIB Dead                 779.   598.     5
## 17 Stage IIIC Alive                 NA     NA     59
## 18 Stage IIIC Dead                 472.   260.     5
## 19 Stage IV   Alive                 NA     NA     11
## 20 Stage IV   Dead                1071.  1155.     9

hhhmmm is that what you expected? Does the standard deviation (\({\tt st\_dev}\)) and count (\(n\)) influence your intepretation?

Adding new variable to your \({\tt tibble}\)

It is often useful to add new columns that are functions of existing columns.

augmented_brca <- mutate(reordered_brca, death_yrs = death_days_to / 365)
augmented_brca <- select(augmented_brca, participant, death_days_to, death_yrs, everything() )
print(augmented_brca, n=15)
## # A tibble: 1,078 x 80
## # Groups:   stage, vital_status [20]
##    participant death_days_to death_yrs stage vital_status id    tss   barcode
##    <chr>               <dbl>     <dbl> <chr> <chr>        <chr> <chr> <chr>  
##  1 A1FG                  577      1.58 Stag… Dead         TCGA… BH    TCGA-B…
##  2 A18P                  921      2.52 Stag… Dead         TCGA… BH    TCGA-B…
##  3 A1FD                 1009      2.76 Stag… Dead         TCGA… BH    TCGA-B…
##  4 A1EU                 1286      3.52 Stag… Dead         TCGA… BH    TCGA-B…
##  5 A03U                 1793      4.91 Stag… Dead         TCGA… AO    TCGA-A…
##  6 A2D9                 1812      4.96 Stag… Dead         TCGA… GM    TCGA-G…
##  7 A18S                 2009      5.50 Stag… Dead         TCGA… BH    TCGA-B…
##  8 A1ET                 2520      6.90 Stag… Dead         TCGA… BH    TCGA-B…
##  9 A18K                 2763      7.57 Stag… Dead         TCGA… BH    TCGA-B…
## 10 A0X0                 3945     10.8  Stag… Dead         TCGA… B6    TCGA-B…
## 11 A209                 3959     10.8  Stag… Dead         TCGA… BH    TCGA-B…
## 12 A0SB                   NA     NA    Stag… Alive        TCGA… A1    TCGA-A…
## 13 A08A                   NA     NA    Stag… Alive        TCGA… A8    TCGA-A…
## 14 A156                   NA     NA    Stag… Alive        TCGA… E2    TCGA-E…
## 15 A095                   NA     NA    Stag… Alive        TCGA… A8    TCGA-A…
## # … with 1,063 more rows, and 72 more variables: bcr_patient_uuid <chr>,
## #   form_completion_date <chr>, birth_days_to <chr>, gender <chr>,
## #   menopause_status <chr>, race <chr>, ethnicity <chr>, tumor_status <chr>,
## #   histologic_diagnosis_other <chr>, initial_pathologic_dx_year <chr>,
## #   age_at_diagnosis <chr>, micromet_detection_by_ihc <chr>,
## #   lymph_nodes_examined_count <chr>, er_status_by_ihc <chr>,
## #   er_status_ihc_Percent_Positive <chr>, pr_status_by_ihc <chr>,
## #   pr_status_ihc_percent_positive <chr>, her2_fish_status <chr>,
## #   her2_copy_number <chr>, histological_type <chr>,
## #   metastatic_tumor_indicator <chr>, tumor <lgl>, ANLN <dbl>, FOXC1 <dbl>,
## #   CDH3 <dbl>, FGFR4 <dbl>, UBE2T <dbl>, NDC80 <dbl>, PGR <dbl>, BIRC5 <dbl>,
## #   ORC6 <dbl>, ESR1 <dbl>, PHGDH <dbl>, PTTG1 <dbl>, MELK <dbl>, NAT1 <dbl>,
## #   CXXC5 <dbl>, BCL2 <dbl>, RRM2 <dbl>, GPR160 <dbl>, EXO1 <dbl>, UBE2C <dbl>,
## #   TYMS <dbl>, KRT5 <dbl>, KRT14 <dbl>, MAPT <dbl>, CDC6 <dbl>, MMP11 <dbl>,
## #   MYBL2 <dbl>, SFRP1 <dbl>, CCNE1 <dbl>, BLVRA <dbl>, BAG1 <dbl>, MLPH <dbl>,
## #   CDC20 <dbl>, CENPF <dbl>, MIA <dbl>, KRT17 <dbl>, FOXA1 <dbl>,
## #   ACTR3B <dbl>, CCNB1 <dbl>, MDM2 <dbl>, MYC <dbl>, CEP55 <dbl>,
## #   SLC39A6 <dbl>, ERBB2 <dbl>, GRB7 <dbl>, KIF2C <dbl>, NUF2 <dbl>,
## #   EGFR <dbl>, MKI67 <dbl>, TMEM45B <dbl>

Complete the Transform \(\rightarrow\) Visualize \(\rightarrow\) Model cycle

Let’s visualize the survival times stratified by TNM Stage.
For clarity, let’s start from the top with \({\tt small\_brca}\).

b0 <- rename(small_brca,  stage = ajcc_pathologic_tumor_stage )
b1 <- filter(b0, (grepl("Stage", stage) & !grepl("Stage X", stage) & tumor==TRUE)) 
b2 <- select(b1, participant, stage, vital_status, death_days_to)
b3 <- filter(b2, vital_status=="Dead")
b4 <- mutate(b3, death_yrs = as.numeric(death_days_to) / 365)
g <- ggplot(data=b4)  +
    geom_point(  aes(x = reorder(participant, death_yrs), y= death_yrs, color=stage), size=1)+
    ggtitle("Survival Times by Stage") +
    xlab("Patient") + ylab("Time to Death (Yrs)") +
    theme(plot.title = element_text(lineheight=.8, face="bold", size = 20)) +
    theme(text = element_text(size=11)) + 
    coord_flip() +
     facet_wrap(~ stage, nrow = 1)

This looks pretty hardcore. We are making progress.

The output


b5 <- group_by(b4, stage)
(b6 <- summarise(b5, n=n(), 
                    mean_death_yrs = mean(death_yrs)))
## `summarise()` ungrouping output (override with `.groups` argument)
## # A tibble: 9 x 3
##   stage          n mean_death_yrs
##   <chr>      <int>          <dbl>
## 1 Stage I       11           5.63
## 2 Stage IA       2           2.72
## 3 Stage IIA     24           4.58
## 4 Stage IIB     20           5.35
## 5 Stage III      1           1.69
## 6 Stage IIIA    18           3.65
## 7 Stage IIIB     5           2.13
## 8 Stage IIIC     5           1.29
## 9 Stage IV       9           2.93

The output

g + geom_hline(yintercept=b6$mean_death_yrs[1], color = "red") +
  geom_hline(yintercept=b6$mean_death_yrs[9], color = "blue")

Challenge

The last \(50\) variables give expression values for \(50\) genes. When I was wrangling this data into a \({\tt tibble}\), I just used the gene name.
Arguably, it would have been better to us variables names of the form \({\tt Gene.ANIN, Gene.FOXC1, Gene.CDH3,}\) etc.
Why? Because this clearly marks these variables as different than the first \(29\) variables which are not gene expression.
If I wanted to add or delete these variables with \({\tt select()}\), I could have used something like the \({\tt starts\_with()}\) function.
Create a \({\tt tibble}\) called \({\tt pure\_expression}\) that contains only the \({\tt participant}\) variables, and the expression of all \(50\) genes, after changing the gene names as discussed above.

Points of Reflection

What advantages or disadvantages are there between traditional spreadsheets and these types of transformations in \({\tt R}\)?
How does the Transform \(\rightarrow\) Visualize \(\rightarrow\) Model cycle relate to Simpson’s paradox?
In the slids above, we focused on removing observations (rows) to reduce the heterogeneity in our dataset. It might be easier to see interesting patterns when technical and nuisance biological variability is reduced. What are the potential downsides of reducing the number of observations?
Although data scientists speak about the Transform \(\rightarrow\) Visualize \(\rightarrow\) Model cycle, what similarities and differences do you see between this cycle and what you experience as a bench scientist?

BIOL480

Computational Biology Concordia