gdcRNAMerge: Merge RNA/miRNAs raw counts data

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

Description

Merge raw counts data that is downloaded from GDC to a single expression matrix

Usage

gdcRNAMerge(metadata, path, data.type, organized = FALSE)

Arguments

metadata	metadata parsed from gdcParseMetadata
path	path to downloaded files for merging
data.type	one of 'RNAseq' and 'miRNAs'
organized	logical, whether the raw counts data have already been organized into a single folder (eg., data downloaded by the 'GenomicDataCommons' method are already organized). Default is FALSE.

Value

A dataframe or numeric matrix of raw counts data with rows are genes or miRNAs and columns are samples

Author(s)

Ruidong Li and Han Qu

Examples

####### Merge RNA expression data #######
metaMatrix <- gdcParseMetadata(project.id='TARGET-RT', 
    data.type='RNAseq')
## Not run: rnaExpr <- gdcRNAMerge(metadata=metaMatrix, path='RNAseq/', 
    data.type='RNAseq')
## End(Not run)

Jialab-UCR/GDCRNATools documentation built on Nov. 28, 2020, 11:23 a.m.