Steps to reproduce the heart failure case study data
# transcripts <- read.csv(here::here("inst", "extdata", "heartFailure", "transcripts.tsv"), header = TRUE, sep = "\t")
# geneSd <- apply(transcripts, 2, sd)
# write.table(transcripts[, order(geneSd, decreasing = TRUE)[1:5000]], file = here::here("inst", "extdata", "caseStudy", "mrna.tsv"), sep = "\t")
omicsData <- lapply(c(" cells.tsv" , " holter.tsv" , " mrna.tsv" , " proteins.tsv" ), function (i ){
read.csv(here :: here(" inst" , " extdata" , " heartFailure" , i ), header = TRUE , sep = " \t " )
})
names(omicsData ) <- c(" cells" , " holter" , " mrna" , " proteins" )
# # save heart failure datasets
heartFailure <- list (
demo = read.csv(here :: here(" inst" , " extdata" , " heartFailure" , " clinical.tsv" ), header = TRUE , sep = " \t " ),
omicsData = omicsData
)
usethis :: use_data(heartFailure , overwrite = TRUE )
## ✔ Setting active project to '/Users/asingh/Documents/omicsBioAnalytics'
## ✔ Saving 'heartFailure' to 'data/heartFailure.rda'
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Catalina 10.15.3
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] knitr_1.24 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3
## [5] purrr_0.3.3 readr_1.3.1 tidyr_0.8.3 tibble_2.1.3
## [9] ggplot2_3.2.1 tidyverse_1.2.1
##
## loaded via a namespace (and not attached):
## [1] clisymbols_1.2.0 tidyselect_0.2.5 xfun_0.9 haven_2.1.1
## [5] lattice_0.20-38 colorspace_1.4-1 generics_0.0.2 vctrs_0.2.1
## [9] htmltools_0.4.0 usethis_1.5.1 yaml_2.2.0 rlang_0.4.0
## [13] pillar_1.4.2 glue_1.3.1 withr_2.1.2 modelr_0.1.5
## [17] readxl_1.3.1 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0
## [21] rvest_0.3.4 evaluate_0.14 broom_0.5.2 Rcpp_1.0.2
## [25] scales_1.0.0 backports_1.1.4 jsonlite_1.6 fs_1.3.1
## [29] hms_0.5.1 digest_0.6.23 stringi_1.4.3 grid_3.6.1
## [33] rprojroot_1.3-2 here_0.1 cli_1.1.0 tools_3.6.1
## [37] magrittr_1.5 lazyeval_0.2.2 crayon_1.3.4 pkgconfig_2.0.2
## [41] zeallot_0.1.0 xml2_1.2.2 lubridate_1.7.4 assertthat_0.2.1
## [45] rmarkdown_1.15 httr_1.4.1 rstudioapi_0.10 R6_2.4.0
## [49] nlme_3.1-140 compiler_3.6.1