CPTACBiolink is an R package to programmatically obtain and analyze multi-omics data generated in the Clinical Proteomic Tumor Analysis Consortium. Currently the archive contains mutliple profiling (including genomics, transcriptiomics, proteomics, phospho-proteimics and others) for more than 12 tumor types.
library(devtools)
install_github("miccec/CPTACBiolinks")
library(CPTACBiolinks)
## GET DATASETS LIST
getDatasetsList()
will produce the list of available cancer dataset
## GET DATA LIST OF CANCER
CancerType = "Endometrial"
getOmicsList(CancerType)
with the function getOmicsList you get all the available data for a specific cancer dataset.
## GET ALL DATASETS OF AN OMICS TYPE FROM CANCER
OmicsType = "Phosphoproteome"
phosphopro = getDataType(CancerType,OmicsType)
Once you have know available data for your project you can download the desired data with the function getDataType you get all the available data for a specific omics type from cancer dataset.
## GET MULTI DATA TYPE OF CANCER
data_type = c("RNAseq (HiSeq, Gene level, Tumor)", "Proteome (Gene level, TMT Unshared Log Ratio, Tumor)")
endometrial_omics = getData(CancerType,data_type)
names(endometrial_omics)
otherwise you can use getData, if you want to download specifics data or all the data, using "All" as parameter to getData.
## GET ALL DATA OF CANCER
all_endometrial = getData(CancerType,"All")
names(all_endometrial)