GDCquery_Maf {TCGAbiolinks} | R Documentation |
GDCquery_Maf uses the following guide to download maf files https://gdc-docs.nci.nih.gov/Data/Release_Notes/Data_Release_Notes/
GDCquery_Maf(tumor, save.csv = FALSE, directory = "GDCdata", pipelines = NULL)
tumor |
a valid tumor |
save.csv |
Write maf file into a csv document |
directory |
Directory/Folder where the data will downloaded. Default: GDCdata |
pipelines |
Four separate variant calling pipelines are implemented for GDC data harmonization. Options: muse, varscan2, somaticsniper, mutect2. For more information: https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/ |
A data frame with the maf file information
## Not run: acc.muse.maf <- GDCquery_Maf("ACC", pipelines = "muse") acc.varscan2.maf <- GDCquery_Maf("ACC", pipelines = "varscan2") acc.somaticsniper.maf <- GDCquery_Maf("ACC", pipelines = "somaticsniper") acc.mutect.maf <- GDCquery_Maf("ACC", pipelines = "mutect2") ## End(Not run)