R/getMAFDataTCGA.R
getMAFdataTCGA.RdThis function download and extract the mutation data in MAF format from TCGA.
A character vector of TCGA cancer codes
path of the file containing the mutation information in the MAF format
type of variant caller in TCGA
A vector containing the path of the downloaded mutation annotation files
library(MAFDash)
cancerCodes <- c("ACC","THCA")
outputFolderPath <- tempdir()
maf <- getMAFdataTCGA(cancerCodes = cancerCodes,outputFolder = outputFolderPath)
#> ============================================================================
#> For more information about MAF data please read the following GDC manual and web pages:
#> GDC manual: https://gdc-docs.nci.nih.gov/Data/PDF/Data_UG.pdf
#> https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
#> https://gdc.cancer.gov/about-gdc/variant-calling-gdc
#> ============================================================================
#> --------------------------------------
#> o GDCquery: Searching in GDC database
#> --------------------------------------
#> Genome of reference: hg38
#> --------------------------------------------
#> oo Accessing GDC. This might take a while...
#> --------------------------------------------
#> ooo Project: TCGA-ACC
#> --------------------
#> oo Filtering results
#> --------------------
#> ooo By access
#> ooo By data.type
#> ooo By workflow.type
#> ----------------
#> oo Checking data
#> ----------------
#> ooo Check if there are duplicated cases
#> ooo Check if there results for the query
#> -------------------
#> o Preparing output
#> -------------------
#> Downloading data for project TCGA-ACC
#> GDCdownload will download: 2.666716 MB
#> Downloading as: TCGA.ACC.mutect.81ac2c46-37db-4dcd-923a-061a7ae626a3.DR-10.0.somatic.maf.gz
#>
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#> ============================================================================
#> For more information about MAF data please read the following GDC manual and web pages:
#> GDC manual: https://gdc-docs.nci.nih.gov/Data/PDF/Data_UG.pdf
#> https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
#> https://gdc.cancer.gov/about-gdc/variant-calling-gdc
#> ============================================================================
#> --------------------------------------
#> o GDCquery: Searching in GDC database
#> --------------------------------------
#> Genome of reference: hg38
#> --------------------------------------------
#> oo Accessing GDC. This might take a while...
#> --------------------------------------------
#> ooo Project: TCGA-THCA
#> --------------------
#> oo Filtering results
#> --------------------
#> ooo By access
#> ooo By data.type
#> ooo By workflow.type
#> ----------------
#> oo Checking data
#> ----------------
#> ooo Check if there are duplicated cases
#> ooo Check if there results for the query
#> -------------------
#> o Preparing output
#> -------------------
#> Downloading data for project TCGA-THCA
#> GDCdownload will download: 2.89136 MB
#> Downloading as: TCGA.THCA.mutect.13999735-2e70-439f-a6d9-45d831ba1a1a.DR-10.0.somatic.maf.gz
#>
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