gdcRNAMerge: Merge RNA/miRNAs raw counts data

Description Usage Arguments Value Author(s) Examples

View source: R/gdcRNAMerge.R

Description

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

Usage

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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

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####### 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)

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