Assignment 1 Answers
Question 1 [7 points]
i. Does Google have the right to look at your emails, documents, drawings or other objects?
Yes [0.5 points]
Does Google have the right to use this information? What is meta-data? Can it collect meta-data about your information?
- Yes [0.5 points]
- Meta-data is data that describes other data [0.5 points]
- Yes [0.5 points]
- Yes [0.5 points]
How can you turn on or off the geographical tracking mechanism associated with your account? + Sign in to google account -> Data & personalization tab -> Web & App activity -> See all Activity Controls -> Location History [1 point]
Are you satisfied with the level of security and user agreement with Google?
- Opinion [4 points]
Question 2 [3 points]
Does cloud computing reduce the overall cost for computers and computation for the “average” person? If so, how? Make reference to the definitions and components of cloud and traditional computing from the lecture notes. 4 or 5 sentences.
- Yes, cloud computing reduce the overall cost for computers and computation for the “average” person [1 point]
- Explanation. Must include definition or at least make distinction between the two paradigms. [2 points/1 point if missing]
Question 3 [3 points]
Give an example of how concepts from computation drifted into the life sciences? 3 or 4 sentences.
+ Good example [1.5 points]
+ Explanation [1.5 points]
Question 4 [3 points]
Argue for and against each of the following items as a computing device (make references to the 3 fundamental properties of modern computers).
- compass
- a car
- an assembly line to make cars at the Ford Inc. factory
Property 1: Input → algorithm → output
Property 2: Notion of reprogrammability
Property 3: Notion of state and memory
Argument for and against for each point worth 0.5 points or 1 point per item if going through three properties for item.
Question 5 [4 points]
What privacy issues might arise in -omic studies? Are the issues of privacy more or less acute in a transcriptome-based study (as we saw in class) than say a genomic DNA-based study (sequencing the genome of individuals)? Remember that both studies are based on sequencing RNA and DNA of samples
Stating a valid privacy issue [2 points]
Stating either genomic/transcriptomic issue with valid conceptual explanation [2 points]
For example: Privacy regarding genomics is more of an issue because most peoples DNA is unique. Therefore, if someone has the DNA of a person, they have a unique identifier of that person, like taking someones fingerprints.
Question 6 [4 points]
Screenshot [2 points]
# [2 points]
library("tidyverse")
## ── Attaching packages ───────────────────────────────────────────── tidyverse 1.3.0 ──
## ✓ ggplot2 3.3.2 ✓ purrr 0.3.4
## ✓ tibble 3.0.3 ✓ dplyr 1.0.1
## ✓ tidyr 1.1.1 ✓ stringr 1.4.0
## ✓ readr 1.3.1 ✓ forcats 0.5.0
## ── Conflicts ──────────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()
load("/cloud/project/data/small_brca.Rdata")
sessionInfo()
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.6 LTS
##
## Matrix products: default
## BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
## LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
##
## locale:
## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.1 purrr_0.3.4
## [5] readr_1.3.1 tidyr_1.1.1 tibble_3.0.3 ggplot2_3.3.2
## [9] tidyverse_1.3.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.5 cellranger_1.1.0 pillar_1.4.6 compiler_4.0.2
## [5] dbplyr_1.4.4 tools_4.0.2 digest_0.6.25 lubridate_1.7.9
## [9] jsonlite_1.7.0 evaluate_0.14 lifecycle_0.2.0 gtable_0.3.0
## [13] pkgconfig_2.0.3 rlang_0.4.7 reprex_0.3.0 cli_2.0.2
## [17] rstudioapi_0.11 DBI_1.1.0 yaml_2.2.1 haven_2.3.1
## [21] xfun_0.16 withr_2.2.0 xml2_1.3.2 httr_1.4.2
## [25] knitr_1.29 fs_1.5.0 hms_0.5.3 generics_0.0.2
## [29] vctrs_0.3.2 grid_4.0.2 tidyselect_1.1.0 glue_1.4.1
## [33] R6_2.4.1 fansi_0.4.1 readxl_1.3.1 rmarkdown_2.3
## [37] modelr_0.1.8 blob_1.2.1 magrittr_1.5 backports_1.1.8
## [41] scales_1.1.1 ellipsis_0.3.1 htmltools_0.5.0 rvest_0.3.6
## [45] assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.6 munsell_0.5.0
## [49] broom_0.7.0 crayon_1.3.4I will also accept, but I don’t like this as much
date(); version## [1] "Wed Sep 30 16:27:19 2020"## _
## platform x86_64-pc-linux-gnu
## arch x86_64
## os linux-gnu
## system x86_64, linux-gnu
## status
## major 4
## minor 0.2
## year 2020
## month 06
## day 22
## svn rev 78730
## language R
## version.string R version 4.0.2 (2020-06-22)
## nickname Taking Off AgainQuestion 7 [5 points]
# [2.5 points]
ggplot(data = small_brca) +
geom_point(mapping = aes(x = GRB7, y = ERBB2, color = her2_fish_status, shape = tumor), size = 2) 
Valid interpretation of the data [2.5 points]
Question 8 [5 points]
Pie charts [1.5 points each]
ggplot (data = small_brca, mapping = aes (x = "", fill = tumor)) +
geom_bar(width = 1) +
coord_polar("y", start=0)
ggplot (data = small_brca, mapping = aes (x = "", fill = her2_fish_status)) +
geom_bar(width = 1) +
coord_polar("y", start=0)
Valid interpretation of the data [2 points]
Question 9 [5 points]
Graph [2.5 points]
ggplot(data = small_brca) +
geom_point(mapping = aes(x = ESR1, y = ERBB2, color = her2_fish_status, shape=er_status_by_ihc), size = 2)
## Warning: Removed 1 rows containing missing values (geom_point).
Valid interpretation of the data [2.5 points]
Question 10 [5 points]
Barplot [2.5 points]
ggplot(data = small_brca) +
geom_bar(mapping = aes(x = ajcc_pathologic_tumor_stage, fill = er_status_by_ihc)) +
theme(axis.text.x = element_text(angle = 60, hjust = 1))
Valid interpretation of the data [2.5 points]
Question 11 [2 points]
Assign logical variables
c1 <- TRUE; c2 <- FALSE; c3 <- TRUE; wife <- TRUE; me <- FALSEThe condition is that at least one of Mike’s children at vegetables
# [2 points]
(c1|c2|c3)## [1] TRUEQuestion 12 [4 points]
The logical expression is TRUE only when all of Mike’s children had vegetables and he and his wife are exhausted
# [4 points]
((c1&c2&c3)&(me&wife)) ## [1] FALSE