RTCGA
package to
download methylation data that are included in
RTCGA.methylation
packageThe 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
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("RTCGA")
or from GitHub
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:
There are many available date times of TCGA data releases. To see them all just type:
Version 1.0 of RTCGA.methylation
package contains
methylation datasets which were released 2015-11-01
. They
were downloaded in the following way (which is mainly copied from http://rtcga.github.io/RTCGA/:
All cohort names can be checked using:
For all cohorts the following code downloads the mRNA data.
NA
files from data2The existance of NA
files mean that there were no
methylation data for these cohorts.
Below is the code that removes unneeded “MANIFEST.txt” file from each methylation cohort folder.
list.files( "data2") %>%
file.path( "data2", .) %>%
sapply(function(x){
file.path(x, list.files(x)) %>%
grep(pattern = "MANIFEST.txt", x = ., value=TRUE) %>%
file.remove()
})
Below is the code that automatically gives the path to files for all
available methylation cohorts types downloaded to data2
folder.
readTCGA
Because of the fact that methylation data are transposed in
downloaded files, there has been prepared special function
readTCGA
to read and transpose data automatically. Code is
below
RTCGA.methylation
packageOV.methylation[1:300,] -> OV.methylation1
OV.methylation[301:612,] -> OV.methylation2
rm(OV.methylation)
grep( "methylation", ls(), value = TRUE) %>%
grep("path", x=., value = TRUE, invert = TRUE) %>%
cat( sep="," ) #can one to id better? as from use_data documentation:
# ... Unquoted names of existing objects to save
devtools::use_data(BRCA.methylation,COAD.methylation,
COADREAD.methylation,GBMLGG.methylation,
GBM.methylation,KIPAN.methylation,
KIRC.methylation,KIRP.methylation,
LAML.methylation,LUAD.methylation,
LUSC.methylation,OV.methylation1,OV.methylation2,
READ.methylation,STAD.methylation,
STES.methylation,UCEC.methylation,
# overwrite = TRUE,
compress="xz")