In RTCGA/RTCGA: The Cancer Genome Atlas Data Integration

library(knitr)
opts_chunk$set(
    comment = "",
    message = FALSE,
    warning = FALSE,
    tidy.opts = list(
        keep.blank.line = TRUE,
        width.cutoff= 150),
    options(width= 150),
    eval = TRUE
)

RTCGA package

The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care.

RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have a benefcial infuence on development of science and improvement of patients' treatment. RTCGA is an open-source R package, available to download from Bioconductor

# source("http://bioconductor.org/biocLite.R")
# biocLite("RTCGA")

or from github

# if (!require(devtools)) {
#    install.packages("devtools")
#    require(devtools)
# }
# biocLite("RTCGA/RTCGA")

Furthermore, RTCGA package transforms TCGA data into form which is convenient to use in R statistical package. Those data transformations can be a part of statistical analysis pipeline which can be more reproducible with RTCGA.

Use cases and examples are shown in RTCGA packages vignettes:

# browseVignettes("RTCGA")

How to download r name data to gain the same datasets as in RTCGA.r name.r gsub('-', '', releaseDate) package?

There are many available date times of TCGA data releases. To see them all just type:

library(RTCGA)
library(magrittr)
# checkTCGA('Dates')

Version r gsub('-', '', releaseDate) of RTCGA.r name.r gsub('-', '', releaseDate) package contains r name datasets which were released r releaseDate. They were downloaded in the following way (which is mainly copied from http://rtcga.github.io/RTCGA/:

Available cohorts

All cohort names can be checked using:

(cohorts <- infoTCGA() %>% 
   rownames() %>% 
   sub("-counts", "", x=.))

For all cohorts the following code downloads the r name data.

Downloading r name files

dir.create( "data2" ) # name of a directory in which data will be stored
sapply( cohorts, function(element){
tryCatch({
downloadTCGA( cancerTypes = element, 
                            dataSet = dataSet,
              destDir = "data2", 
              date = releaseDate )},
error = function(cond){
   cat("Error: Maybe there weren't", name, " data for ", element, " cancer.\n")
}
)
})

Reading downloaded r name dataset

Shortening paths and directories

list.files( "data2") %>% 
   file.path( "data2", .) %>%
   file.rename( to = substr(.,start=1,stop=50))

Removing NA files from data2 folder

If there were no r name data for some cohorts we should remove corresponding NA files.

list.files( "data2") %>%
   file.path( "data2", .) %>%
   sapply(function(x){
      if (x == "data2/NA")
         file.remove(x)      
   })

Paths to r name data

Below is the code that automatically assigns paths to files for all r name files for all available cohorts types downloaded to data2 folder.

cohorts %>%
    sapply(function(z){
        list.files("data2") %>%
            file.path("data2", .) %>%
            grep(paste0("_",z,"\\."), x = ., value = TRUE) %>%
            file.path(., list.files(.)) %>%
            grep("dataSetFile", x = ., value = TRUE) %>%
            assign(value = .,
                         x = paste0(z, ".",name,".path"),
                         envir = .GlobalEnv)
    })

Reading r name data using readTCGA

Because of the fact that r name data are transposed in downloaded files, there has been prepared special function readTCGA to read (with data.table::fread) and transpose data automatically. Code is below

ls() %>%
   grep(paste0(name,"\\.path"), x = ., value = TRUE) %>% 
   sapply(function(element){
      tryCatch({
         readTCGA(get(element, envir = .GlobalEnv),
               dataType = "dataType") -> read_file

             ## remove non-ASCII strings:
             for( i in 1:ncol(read_file)){
               read_file[, i] <- iconv(read_file[, i],
                                            "UTF-8", "ASCII", sub="")
             } 

         assign(value = read_file,
                x = sub("\\.path", "", x = element),
                envir = .GlobalEnv )
      }, error = function(cond){
        cat(element)
      })
     invisible(NULL)
    }    
)

Saving r name data to RTCGA.r name.r gsub('-', '', releaseDate) package

grep( name, ls(), value = TRUE) %>%
   grep("path", x=., value = TRUE, invert = TRUE) %>%
   paste0( collapse="," ) -> use_data_input
   # ...    Unquoted names of existing objects to save
eval(parse(text=
   paste0("devtools::use_data(",use_data_input,",pkg='../',compress=\"xz\")")
))

RTCGA/RTCGA documentation built on Nov. 1, 2022, 8:15 p.m.