gdcParseMetadata: Parse metadata

In GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Description

Parse metadata either by providing the .json file that is downloaded from GDC cart or by parse metadata automatically by providing the projct id and data type

Usage

gdcParseMetadata(metafile = NULL, project.id, data.type,
  write.meta = FALSE)

Arguments

metafile	metadata file in .json format download from GDC cart. If provided, the metadata will be parsed from this file, otherwise, project and data.type arguments should be provided to retrieve metadata automatically. Default is NULL
project.id	project id in GDC
data.type	one of 'RNAseq' and 'miRNAs'
write.meta	logical, whether to write the metadata to a .json file

Value

A dataframe of metadata containing file_name, sample_id, etc. as well as some basic clinical data

Author(s)

Ruidong Li and Han Qu

Examples

####### Merge RNA expression data #######
metaMatrix <- gdcParseMetadata(project.id='TARGET-RT', data.type='RNAseq')

GDCRNATools documentation built on Nov. 27, 2020, 2 a.m.