GDCquery_ATAC_seq: Retrieve open access ATAC-seq files from GDC server

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Description

Retrieve open access ATAC-seq files from GDC server https://gdc.cancer.gov/about-data/publications/ATACseq-AWG Manifest available at: https://gdc.cancer.gov/files/public/file/ATACseq-AWG_Open_GDC-Manifest.txt

Usage

GDCquery_ATAC_seq(tumor = NULL, file.type = NULL)

Arguments

tumor	a valid tumor
file.type	Write maf file into a csv document

Value

A data frame with the maf file information

Examples

 query <- GDCquery_ATAC_seq(file.type = "txt")
## Not run: 
   GDCdownload(query)

## End(Not run)
query <- GDCquery_ATAC_seq(tumor = "BRCA",file.type = "bigWigs")
## Not run: 
   GDCdownload(query,method = "client")

## End(Not run)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.