R/dataexplore.R
In Wei-V-Zhou/KMPPc: KMPPc: K-M Plot for Pan-cancer
Defines functions
dataexplore
Documented in
dataexplore
#' dataexplore
#'
#' dataexplore for TCGA
#'
#' By default, this function first input cancerType such as "BreastCancer" to explore the dataset whatever you like.
#'
#' @param cancerType The cancertype you'd like to explore, including "BreastCancer", "PancreaticCancer", "Glioma"
#' @param studyId This argument you can explore by yourself, because there is too many researches or database you can take advantage of.
#' @param dataType It provides "mrna", "CNA", "mutation" for more information to dig.
#' @return There is a RData file (survival_inputdata.Rdata) exported to the data folder.
#' @export
#' @import cgdsr
#' @author Wei Zhou <247328181@@qq.com>
#' @examples
#' \dontrun{
#' ## Explore the interested dataset by input the specified cancertype
#' dataexplore(cancerType = "BreastCancer", dataType = "mrna")
#'
#' ## If you have interested datatype, you can input, such as mrna, CNA, mutation, etc
#' dataexplore(cancerType = "BreastCancer", studyId = NULL, dataType = "mrna")
#' }
dataexplore <- function(cancerType, studyId = NULL, dataType = NULL) {
## 0. prepare environment and load libraries
# rm(list = ls())
# gc()
# set.seed(12345)
# graphics.off()
# options(stringsAsFactors = FALSE)
# load packages
# pkgs <- c("cgdsr", "ggplot2", "stringr", "ggpubr", "survival",
# "survminer", "readxl", "ggstatsplot", "export")
# installpkgs <- function(pkgs){
# new.pkgs <- pkgs[!(pkgs %in% installed.packages()[ , "Package"])]
# if (length(new.pkgs))
# BiocManager::install(new.pkgs, ask = F, update = F)
# sapply(pkgs, require, character.only = T)
# }
# installpkgs(pkgs)
# lapply(pkgs, library, character.only = T)
## 1. connect the TCGA database and obtain the data
# create a CGDS connection objext
mycgds <- CGDS("http://www.cbioportal.org/")
# set verbose options to debug and troubleshoot issues
setVerbose(mycgds, TRUE)
# guarantee the unauthorized accessment
mysecurecgds <- CGDS("http://cbioportal.mskcc.org/",
token = "fd0522cb-7972-40d0-9d83-cb4c14e8a337")
# get list of cancer studies at server for view to choose
cancerstudy <- getCancerStudies(mycgds)
if(cancerType == "BreastCancer"){
cancerid <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "brca"))), 1]
studydoi <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "brca"))), 2]
} else if (cancerType == "PancreaticCancer") {
cancerid <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "paad"))), 1]
studydoi <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "paad"))), 2]
} else if (cancerType == "Glioma") {
cancerid <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "glioma|lgg"))), 1]
studydoi <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "glioma|lgg"))), 2]
}
# get available case lists for a given cancer study
if(is.null(studyId)){
MainstrId <- cbind(cancerid, studydoi)
print.table(studydoi, right = F, justify = "centre")
if(interactive()){
repeat{
ANSWER <- readline("Please input the dataset number: ")
num <- as.numeric(ANSWER)
if(is.na(num) || num <= 0 || num > length(studydoi)){
print("Please type right number format!")
} else if (num > 0 && num <= length(studydoi)) {
break;
}
}
}
MainstrDat <- cancerid[num]
} else if (is.numeric(studyId)) {
MainstrDat <- cancerid[as.numeric(studyId)]
} else {
stop("Please input right format studyId!")
}
# get available genetic profiles
mygeneticprofile <- getGeneticProfiles(mycgds, MainstrDat)
if (dataType == "mrna") {
# mrna data
mrnaFile <- grep("mrna", mygeneticprofile[ , 1])
print.table(mygeneticprofile[mrnaFile, 3], right = F, justify = "left")
repeat{
ANSWER <- readline("Please input your interested genetic file number: ")
mrnaNum <- as.numeric(ANSWER)
if (is.na(mrnaNum) || mrnaNum <= 0 || mrnaNum > length(mrnaFile)) {
print("Please type right number format!")
} else if (mrnaNum > 0 && mrnaNum <= length(mrnaFile)) {
break;
}
}
dataTypeFile = mrnaFile[mrnaNum]
} else if (dataType == "methylation") {
# methylation data
methylationFile <- grep("methylation", mygeneticprofile[ , 1])
print.table(mygeneticprofile[methylationFile, 3], right = F, justify = "left")
repeat{
ANSWER <- readline("Please input your interested genetic file number: ")
methylationNum <- as.numeric(ANSWER)
if (is.na(methylationNum) || methylationNum <= 0 || methylationNum > length(methylationFile)) {
print("Please type right number format!")
} else if (methylationNum > 0 && methylationNum <= length(methylationFile)) {
break;
}
}
dataTypeFile = methylationFile[methylationNum]
} else if (dataType == "CNA") {
# CNA data
cnaFile <- grep("CNA", mygeneticprofile[ , 1])
print.table(mygeneticprofile[cnaFile, 3], right = F, justify = "left")
repeat{
ANSWER <- readline("Please input your interested genetic file number: ")
cnaNum <- as.numeric(ANSWER)
if (is.na(cnaNum) || cnaNum <= 0 || cnaNum > length(cnaFile)) {
print("Please type right number format!")
} else if (cnaNum > 0 && cnaNum <= length(cnaFile)) {
break;
}
}
dataTypeFile = cnaFile[cnaNum]
} else if (dataType == "mutation") {
# mutation
mutationFile <- grep("mutation", mygeneticprofile[ , 1])
print.table(mygeneticprofile[mutationFile, 3], right = F, justify = "left")
repeat{
ANSWER <- readline("Please input your interested number: ")
mutationNum <- as.numeric(ANSWER)
if (is.na(mutationNum) || mutationNum <= 0 || mutationNum > length(mutationFile)) {
print("Please type right number format!")
} else if (mutationNum > 0 && mutationNum <= length(mutationFile)) {
break;
}
}
dataTypeFile = mutationFile[mutationNum]
} else {
stop("Please input right format dataType!")
}
geneticFile <- getGeneticProfiles(mycgds, MainstrDat)[dataTypeFile, 1]
# get available genecase list
mycaselist <- getCaseLists(mycgds, MainstrDat)
if (dataType == "mrna") {
# mRNA data
mrnaList <- grep("mrna", mycaselist[ , 1])
print.table(mycaselist[mrnaList, 3], right = F, justify = "centre")
repeat{
ANSWER <- readline("Please input your interested case list number: ")
mrnaNum <- as.numeric(ANSWER)
if (is.na(mrnaNum) || mrnaNum <= 0 || mrnaNum > length(mrnaList)) {
print("Please type right number format!")
} else if (mrnaNum > 0 && mrnaNum <= length(mrnaList)) {
break;
}
}
dataTypeList = mrnaList[mrnaNum]
} else if (dataType == "methylation") {
# methylation data
methylationList <- grep("methylation", mycaselist[ , 1])
print.table(mycaselist[methylationList, 3], right = F, justify = "centre")
repeat{
ANSWER <- readline("Please input your interested case list number: ")
methylationNum <- as.numeric(ANSWER)
if (is.na(methylationNum) || methylationNum <= 0 || methylationNum > length(methylationList)) {
print("Please type right number format!")
} else if (methylationNum > 0 && methylationNum <= length(methylationList)) {
break;
}
}
dataTypeList = methylationList[methylationNum]
} else if (dataType == "CNA") {
# CNA data
cnaList <- grep("CNA", mycaselist[ , 2])
print.table(mycaselist[cnaList, 3], right = F, justify = "centre")
repeat{
ANSWER <- readline("Please input your interested case list number: ")
cnaNum <- as.numeric(ANSWER)
if (is.na(cnaNum) || cnaNum <= 0 || cnaNum > length(cnaList)) {
print("Please type right number format!")
} else if (cnaNum > 0 && cnaNum <= length(cnaList)) {
break;
}
}
dataTypeList = cnaList[cnaNum]
} else if (dataType == "mutation") {
# mutation
mutationList <- grep("mutation", mycaselist[ , 2])
print.table(mycaselist[mutationList, 3], right = F, justify = "centre")
repeat{
ANSWER <- readline("Please input your interested case list number: ")
mutationNum <- as.numeric(ANSWER)
if (is.na(mutationNum) || mutationNum <= 0 || mutationNum > length(mutationList)) {
print("Please type right number format!")
} else if (mutationNum > 0 && mutationNum <= length(mutationList)) {
break;
}
}
dataTypeList = mutationList[mutationNum]
} else {
stop("Please input right format dataType!")
}
caseList <- getCaseLists(mycgds, MainstrDat)[dataTypeList, 1]
# get data slices for a specified list of genes, genetic profiles and case list
repeat{
ANSWER <- readline("Please input your interested gene name: ")
geneName <- toupper(ANSWER)
if (geneName == "") {
print("Please type right number format!")
} else {
break;
}
}
exprSet = getProfileData(mycgds, geneName, geneticFile, caseList)
# get clinical data for the case list
myclinicaldata <- getClinicalData(mycgds, caseList)
# save the data
save(exprSet, myclinicaldata, file="../data/survival_inputdata.Rdata")
}
# sessionInfo()
# R version 3.6.3 (2020-02-29)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 18363)
#
# Matrix products: default
#
# locale:
# [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
# [3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
# [5] LC_TIME=Chinese (Simplified)_China.936
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] export_0.2.2 ggstatsplot_0.1.3 readxl_1.3.1 survminer_0.4.6 survival_3.1-8
# [6] ggpubr_0.2.4 magrittr_1.5 stringr_1.4.0 ggplot2_3.2.1 cgdsr_1.3.0
#
# loaded via a namespace (and not attached):
# [1] tidyselect_0.2.5 lme4_1.1-21 robust_0.4-18.1
# [4] htmlwidgets_1.5.1 grid_3.6.3 munsell_0.5.0
# [7] codetools_0.2-16 future_1.15.1 miniUI_0.1.1.1
# [10] withr_2.1.2 Brobdingnag_1.2-6 metaBMA_0.6.2
# [13] colorspace_1.4-1 uuid_0.1-2 knitr_1.26
# [16] rstudioapi_0.10 stats4_3.6.3 DescTools_0.99.30
# [19] robustbase_0.93-5 officer_0.3.6 ggsignif_0.6.0
# [22] rcompanion_2.3.7 listenv_0.7.0 emmeans_1.4.2
# [25] rstan_2.19.2 repr_1.0.1 mnormt_1.5-5
# [28] KMsurv_0.1-5 MCMCpack_1.4-4 bridgesampling_0.7-2
# [31] coda_0.19-3 vctrs_0.2.0 generics_0.0.2
# [34] TH.data_1.0-10 metafor_2.1-0 xfun_0.11
# [37] R6_2.4.1 BayesFactor_0.9.12-4.2 manipulateWidget_0.10.0
# [40] reshape_0.8.8 logspline_2.1.15 assertthat_0.2.1
# [43] promises_1.1.0 scales_1.1.0 multcomp_1.4-10
# [46] ggExtra_0.9 gtable_0.3.0 multcompView_0.1-7
# [49] globals_0.12.4 processx_3.4.1 mcmc_0.9-6
# [52] sandwich_2.5-1 rlang_0.4.1 MatrixModels_0.4-1
# [55] EMT_1.1 zeallot_0.1.0 systemfonts_0.1.1
# [58] splines_3.6.3 TMB_1.7.16 lazyeval_0.2.2
# [61] broom_0.5.2 inline_0.3.15 rgl_0.100.30
# [64] reshape2_1.4.3 abind_1.4-5 modelr_0.1.5
# [67] crosstalk_1.0.0 backports_1.1.5 httpuv_1.5.2
# [70] rsconnect_0.8.16 tools_3.6.3 psych_1.8.12
# [73] ellipsis_0.3.0 stargazer_5.2.2 WRS2_1.0-0
# [76] ez_4.4-0 Rcpp_1.0.3 plyr_1.8.4
# [79] base64enc_0.1-3 jmvcore_1.0.8 purrr_0.3.3
# [82] ps_1.3.0 prettyunits_1.0.2 pbapply_1.4-2
# [85] cowplot_1.0.0 zoo_1.8-6 LaplacesDemon_16.1.1
# [88] haven_2.2.0 ggrepel_0.8.1 cluster_2.1.0
# [91] furrr_0.1.0 data.table_1.12.6 openxlsx_4.1.3
# [94] flextable_0.5.6 SparseM_1.77 lmtest_0.9-37
# [97] mvtnorm_1.0-11 broomExtra_0.0.6 sjmisc_2.8.2
# [100] matrixStats_0.54.0 evaluate_0.14 hms_0.5.2
# [103] mime_0.9 xtable_1.8-4 rio_0.5.16
# [106] sjstats_0.17.7 pairwiseComparisons_0.1.2 broom.mixed_0.2.4
# [109] gridExtra_2.3 rstantools_2.0.0 compiler_3.6.3
# [112] tibble_2.1.3 crayon_1.3.4 minqa_1.2.4
# [115] R.oo_1.23.0 StanHeaders_2.19.0 htmltools_0.4.0
# [118] mgcv_1.8-31 mc2d_0.1-18 pcaPP_1.9-73
# [121] later_1.0.0 libcoin_1.0-5 tidyr_1.0.0
# [124] rrcov_1.4-7 expm_0.999-4 sjlabelled_1.1.1
# [127] jmv_1.0.8 MASS_7.3-51.4 boot_1.3-23
# [130] Matrix_1.2-18 car_3.0-5 cli_1.1.0
# [133] R.methodsS3_1.7.1 parallel_3.6.3 insight_0.7.0
# [136] forcats_0.4.0 pkgconfig_2.0.3 km.ci_0.5-2
# [139] fit.models_0.5-14 statsExpressions_0.1.1 coin_1.3-1
# [142] foreign_0.8-72 skimr_2.0.1 xml2_1.2.2
# [145] paletteer_0.2.1 ggcorrplot_0.1.3 webshot_0.5.2
# [148] rvg_0.2.2 estimability_1.3 callr_3.3.2
# [151] digest_0.6.25 parameters_0.3.0 rmarkdown_1.17
# [154] cellranger_1.1.0 survMisc_0.5.5 nortest_1.0-4
# [157] gdtools_0.2.1 curl_4.2 modeltools_0.2-22
# [160] shiny_1.4.0.2 gtools_3.8.1 quantreg_5.52
# [163] rjson_0.2.20 nloptr_1.2.1 lifecycle_0.1.0
# [166] nlme_3.1-142 jsonlite_1.6.1 carData_3.0-3
# [169] groupedstats_0.1.0 pillar_1.4.2 lattice_0.20-38
# [172] loo_2.1.0 fastmap_1.0.1 DEoptimR_1.0-8
# [175] pkgbuild_1.0.6 glue_1.3.1 bayestestR_0.4.0
# [178] zip_2.0.4 stringi_1.4.3 performance_0.4.0
# [181] rsample_0.0.5 dplyr_0.8.3
#============================#
# Musician: Resonance #
# Date: 2020/03/16 #
# Revised author: Resonance #
# 1st Time: 2020/03/17 #
# 2nd Time: 2020/05/27 #
#============================#
Wei-V-Zhou/KMPPc documentation built on Sept. 5, 2020, 6:21 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions dataexplore
Documented in dataexplore
#' dataexplore
#'
#' dataexplore for TCGA
#'
#' By default, this function first input cancerType such as "BreastCancer" to explore the dataset whatever you like.
#'
#' @param cancerType The cancertype you'd like to explore, including "BreastCancer", "PancreaticCancer", "Glioma"
#' @param studyId This argument you can explore by yourself, because there is too many researches or database you can take advantage of.
#' @param dataType It provides "mrna", "CNA", "mutation" for more information to dig.
#' @return There is a RData file (survival_inputdata.Rdata) exported to the data folder.
#' @export
#' @import cgdsr
#' @author Wei Zhou <247328181@@qq.com>
#' @examples
#' \dontrun{
#' ## Explore the interested dataset by input the specified cancertype
#' dataexplore(cancerType = "BreastCancer", dataType = "mrna")
#'
#' ## If you have interested datatype, you can input, such as mrna, CNA, mutation, etc
#' dataexplore(cancerType = "BreastCancer", studyId = NULL, dataType = "mrna")
#' }
dataexplore <- function(cancerType, studyId = NULL, dataType = NULL) {
## 0. prepare environment and load libraries
# rm(list = ls())
# gc()
# set.seed(12345)
# graphics.off()
# options(stringsAsFactors = FALSE)
# load packages
# pkgs <- c("cgdsr", "ggplot2", "stringr", "ggpubr", "survival",
# "survminer", "readxl", "ggstatsplot", "export")
# installpkgs <- function(pkgs){
# new.pkgs <- pkgs[!(pkgs %in% installed.packages()[ , "Package"])]
# if (length(new.pkgs))
# BiocManager::install(new.pkgs, ask = F, update = F)
# sapply(pkgs, require, character.only = T)
# }
# installpkgs(pkgs)
# lapply(pkgs, library, character.only = T)
## 1. connect the TCGA database and obtain the data
# create a CGDS connection objext
mycgds <- CGDS("http://www.cbioportal.org/")
# set verbose options to debug and troubleshoot issues
setVerbose(mycgds, TRUE)
# guarantee the unauthorized accessment
mysecurecgds <- CGDS("http://cbioportal.mskcc.org/",
token = "fd0522cb-7972-40d0-9d83-cb4c14e8a337")
# get list of cancer studies at server for view to choose
cancerstudy <- getCancerStudies(mycgds)
if(cancerType == "BreastCancer"){
cancerid <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "brca"))), 1]
studydoi <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "brca"))), 2]
} else if (cancerType == "PancreaticCancer") {
cancerid <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "paad"))), 1]
studydoi <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "paad"))), 2]
} else if (cancerType == "Glioma") {
cancerid <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "glioma|lgg"))), 1]
studydoi <- cancerstudy[which(!is.na(str_extract(cancerstudy[ , 1], "glioma|lgg"))), 2]
}
# get available case lists for a given cancer study
if(is.null(studyId)){
MainstrId <- cbind(cancerid, studydoi)
print.table(studydoi, right = F, justify = "centre")
if(interactive()){
repeat{
ANSWER <- readline("Please input the dataset number: ")
num <- as.numeric(ANSWER)
if(is.na(num) || num <= 0 || num > length(studydoi)){
print("Please type right number format!")
} else if (num > 0 && num <= length(studydoi)) {
break;
}
}
}
MainstrDat <- cancerid[num]
} else if (is.numeric(studyId)) {
MainstrDat <- cancerid[as.numeric(studyId)]
} else {
stop("Please input right format studyId!")
}
# get available genetic profiles
mygeneticprofile <- getGeneticProfiles(mycgds, MainstrDat)
if (dataType == "mrna") {
# mrna data
mrnaFile <- grep("mrna", mygeneticprofile[ , 1])
print.table(mygeneticprofile[mrnaFile, 3], right = F, justify = "left")
repeat{
ANSWER <- readline("Please input your interested genetic file number: ")
mrnaNum <- as.numeric(ANSWER)
if (is.na(mrnaNum) || mrnaNum <= 0 || mrnaNum > length(mrnaFile)) {
print("Please type right number format!")
} else if (mrnaNum > 0 && mrnaNum <= length(mrnaFile)) {
break;
}
}
dataTypeFile = mrnaFile[mrnaNum]
} else if (dataType == "methylation") {
# methylation data
methylationFile <- grep("methylation", mygeneticprofile[ , 1])
print.table(mygeneticprofile[methylationFile, 3], right = F, justify = "left")
repeat{
ANSWER <- readline("Please input your interested genetic file number: ")
methylationNum <- as.numeric(ANSWER)
if (is.na(methylationNum) || methylationNum <= 0 || methylationNum > length(methylationFile)) {
print("Please type right number format!")
} else if (methylationNum > 0 && methylationNum <= length(methylationFile)) {
break;
}
}
dataTypeFile = methylationFile[methylationNum]
} else if (dataType == "CNA") {
# CNA data
cnaFile <- grep("CNA", mygeneticprofile[ , 1])
print.table(mygeneticprofile[cnaFile, 3], right = F, justify = "left")
repeat{
ANSWER <- readline("Please input your interested genetic file number: ")
cnaNum <- as.numeric(ANSWER)
if (is.na(cnaNum) || cnaNum <= 0 || cnaNum > length(cnaFile)) {
print("Please type right number format!")
} else if (cnaNum > 0 && cnaNum <= length(cnaFile)) {
break;
}
}
dataTypeFile = cnaFile[cnaNum]
} else if (dataType == "mutation") {
# mutation
mutationFile <- grep("mutation", mygeneticprofile[ , 1])
print.table(mygeneticprofile[mutationFile, 3], right = F, justify = "left")
repeat{
ANSWER <- readline("Please input your interested number: ")
mutationNum <- as.numeric(ANSWER)
if (is.na(mutationNum) || mutationNum <= 0 || mutationNum > length(mutationFile)) {
print("Please type right number format!")
} else if (mutationNum > 0 && mutationNum <= length(mutationFile)) {
break;
}
}
dataTypeFile = mutationFile[mutationNum]
} else {
stop("Please input right format dataType!")
}
geneticFile <- getGeneticProfiles(mycgds, MainstrDat)[dataTypeFile, 1]
# get available genecase list
mycaselist <- getCaseLists(mycgds, MainstrDat)
if (dataType == "mrna") {
# mRNA data
mrnaList <- grep("mrna", mycaselist[ , 1])
print.table(mycaselist[mrnaList, 3], right = F, justify = "centre")
repeat{
ANSWER <- readline("Please input your interested case list number: ")
mrnaNum <- as.numeric(ANSWER)
if (is.na(mrnaNum) || mrnaNum <= 0 || mrnaNum > length(mrnaList)) {
print("Please type right number format!")
} else if (mrnaNum > 0 && mrnaNum <= length(mrnaList)) {
break;
}
}
dataTypeList = mrnaList[mrnaNum]
} else if (dataType == "methylation") {
# methylation data
methylationList <- grep("methylation", mycaselist[ , 1])
print.table(mycaselist[methylationList, 3], right = F, justify = "centre")
repeat{
ANSWER <- readline("Please input your interested case list number: ")
methylationNum <- as.numeric(ANSWER)
if (is.na(methylationNum) || methylationNum <= 0 || methylationNum > length(methylationList)) {
print("Please type right number format!")
} else if (methylationNum > 0 && methylationNum <= length(methylationList)) {
break;
}
}
dataTypeList = methylationList[methylationNum]
} else if (dataType == "CNA") {
# CNA data
cnaList <- grep("CNA", mycaselist[ , 2])
print.table(mycaselist[cnaList, 3], right = F, justify = "centre")
repeat{
ANSWER <- readline("Please input your interested case list number: ")
cnaNum <- as.numeric(ANSWER)
if (is.na(cnaNum) || cnaNum <= 0 || cnaNum > length(cnaList)) {
print("Please type right number format!")
} else if (cnaNum > 0 && cnaNum <= length(cnaList)) {
break;
}
}
dataTypeList = cnaList[cnaNum]
} else if (dataType == "mutation") {
# mutation
mutationList <- grep("mutation", mycaselist[ , 2])
print.table(mycaselist[mutationList, 3], right = F, justify = "centre")
repeat{
ANSWER <- readline("Please input your interested case list number: ")
mutationNum <- as.numeric(ANSWER)
if (is.na(mutationNum) || mutationNum <= 0 || mutationNum > length(mutationList)) {
print("Please type right number format!")
} else if (mutationNum > 0 && mutationNum <= length(mutationList)) {
break;
}
}
dataTypeList = mutationList[mutationNum]
} else {
stop("Please input right format dataType!")
}
caseList <- getCaseLists(mycgds, MainstrDat)[dataTypeList, 1]
# get data slices for a specified list of genes, genetic profiles and case list
repeat{
ANSWER <- readline("Please input your interested gene name: ")
geneName <- toupper(ANSWER)
if (geneName == "") {
print("Please type right number format!")
} else {
break;
}
}
exprSet = getProfileData(mycgds, geneName, geneticFile, caseList)
# get clinical data for the case list
myclinicaldata <- getClinicalData(mycgds, caseList)
# save the data
save(exprSet, myclinicaldata, file="../data/survival_inputdata.Rdata")
}
# sessionInfo()
# R version 3.6.3 (2020-02-29)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 18363)
#
# Matrix products: default
#
# locale:
# [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
# [3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
# [5] LC_TIME=Chinese (Simplified)_China.936
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] export_0.2.2 ggstatsplot_0.1.3 readxl_1.3.1 survminer_0.4.6 survival_3.1-8
# [6] ggpubr_0.2.4 magrittr_1.5 stringr_1.4.0 ggplot2_3.2.1 cgdsr_1.3.0
#
# loaded via a namespace (and not attached):
# [1] tidyselect_0.2.5 lme4_1.1-21 robust_0.4-18.1
# [4] htmlwidgets_1.5.1 grid_3.6.3 munsell_0.5.0
# [7] codetools_0.2-16 future_1.15.1 miniUI_0.1.1.1
# [10] withr_2.1.2 Brobdingnag_1.2-6 metaBMA_0.6.2
# [13] colorspace_1.4-1 uuid_0.1-2 knitr_1.26
# [16] rstudioapi_0.10 stats4_3.6.3 DescTools_0.99.30
# [19] robustbase_0.93-5 officer_0.3.6 ggsignif_0.6.0
# [22] rcompanion_2.3.7 listenv_0.7.0 emmeans_1.4.2
# [25] rstan_2.19.2 repr_1.0.1 mnormt_1.5-5
# [28] KMsurv_0.1-5 MCMCpack_1.4-4 bridgesampling_0.7-2
# [31] coda_0.19-3 vctrs_0.2.0 generics_0.0.2
# [34] TH.data_1.0-10 metafor_2.1-0 xfun_0.11
# [37] R6_2.4.1 BayesFactor_0.9.12-4.2 manipulateWidget_0.10.0
# [40] reshape_0.8.8 logspline_2.1.15 assertthat_0.2.1
# [43] promises_1.1.0 scales_1.1.0 multcomp_1.4-10
# [46] ggExtra_0.9 gtable_0.3.0 multcompView_0.1-7
# [49] globals_0.12.4 processx_3.4.1 mcmc_0.9-6
# [52] sandwich_2.5-1 rlang_0.4.1 MatrixModels_0.4-1
# [55] EMT_1.1 zeallot_0.1.0 systemfonts_0.1.1
# [58] splines_3.6.3 TMB_1.7.16 lazyeval_0.2.2
# [61] broom_0.5.2 inline_0.3.15 rgl_0.100.30
# [64] reshape2_1.4.3 abind_1.4-5 modelr_0.1.5
# [67] crosstalk_1.0.0 backports_1.1.5 httpuv_1.5.2
# [70] rsconnect_0.8.16 tools_3.6.3 psych_1.8.12
# [73] ellipsis_0.3.0 stargazer_5.2.2 WRS2_1.0-0
# [76] ez_4.4-0 Rcpp_1.0.3 plyr_1.8.4
# [79] base64enc_0.1-3 jmvcore_1.0.8 purrr_0.3.3
# [82] ps_1.3.0 prettyunits_1.0.2 pbapply_1.4-2
# [85] cowplot_1.0.0 zoo_1.8-6 LaplacesDemon_16.1.1
# [88] haven_2.2.0 ggrepel_0.8.1 cluster_2.1.0
# [91] furrr_0.1.0 data.table_1.12.6 openxlsx_4.1.3
# [94] flextable_0.5.6 SparseM_1.77 lmtest_0.9-37
# [97] mvtnorm_1.0-11 broomExtra_0.0.6 sjmisc_2.8.2
# [100] matrixStats_0.54.0 evaluate_0.14 hms_0.5.2
# [103] mime_0.9 xtable_1.8-4 rio_0.5.16
# [106] sjstats_0.17.7 pairwiseComparisons_0.1.2 broom.mixed_0.2.4
# [109] gridExtra_2.3 rstantools_2.0.0 compiler_3.6.3
# [112] tibble_2.1.3 crayon_1.3.4 minqa_1.2.4
# [115] R.oo_1.23.0 StanHeaders_2.19.0 htmltools_0.4.0
# [118] mgcv_1.8-31 mc2d_0.1-18 pcaPP_1.9-73
# [121] later_1.0.0 libcoin_1.0-5 tidyr_1.0.0
# [124] rrcov_1.4-7 expm_0.999-4 sjlabelled_1.1.1
# [127] jmv_1.0.8 MASS_7.3-51.4 boot_1.3-23
# [130] Matrix_1.2-18 car_3.0-5 cli_1.1.0
# [133] R.methodsS3_1.7.1 parallel_3.6.3 insight_0.7.0
# [136] forcats_0.4.0 pkgconfig_2.0.3 km.ci_0.5-2
# [139] fit.models_0.5-14 statsExpressions_0.1.1 coin_1.3-1
# [142] foreign_0.8-72 skimr_2.0.1 xml2_1.2.2
# [145] paletteer_0.2.1 ggcorrplot_0.1.3 webshot_0.5.2
# [148] rvg_0.2.2 estimability_1.3 callr_3.3.2
# [151] digest_0.6.25 parameters_0.3.0 rmarkdown_1.17
# [154] cellranger_1.1.0 survMisc_0.5.5 nortest_1.0-4
# [157] gdtools_0.2.1 curl_4.2 modeltools_0.2-22
# [160] shiny_1.4.0.2 gtools_3.8.1 quantreg_5.52
# [163] rjson_0.2.20 nloptr_1.2.1 lifecycle_0.1.0
# [166] nlme_3.1-142 jsonlite_1.6.1 carData_3.0-3
# [169] groupedstats_0.1.0 pillar_1.4.2 lattice_0.20-38
# [172] loo_2.1.0 fastmap_1.0.1 DEoptimR_1.0-8
# [175] pkgbuild_1.0.6 glue_1.3.1 bayestestR_0.4.0
# [178] zip_2.0.4 stringi_1.4.3 performance_0.4.0
# [181] rsample_0.0.5 dplyr_0.8.3
#============================#
# Musician: Resonance #
# Date: 2020/03/16 #
# Revised author: Resonance #
# 1st Time: 2020/03/17 #
# 2nd Time: 2020/05/27 #
#============================#
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.