sumDuplicates: Sum all read counts for multiple instances of a single gene...

In RGLab/RNASeqPipelineR: Construct Standardized pipelines for processing RNASeq data

Description

A gene symbol can map to multiple UCSC gene cluster ids so in those instances all read counts mapped to a single gene symbol are summed. The summed read counts are returned in an Expression Set along with the feature data table and optionally an experimental design table.

Usage

sumDuplicates(counts, fDat, cDat = NULL)

Arguments

counts	matrix table of read counts or tpms. Rows are genes and columns are samples
fDat	data.frame feature data - rows map to counts rows
cDat	data.frame. experimental design or phenotype data - rows map to counts columns

Value

ExpressionSet containing the summed counts data (counts), the feature data which will map to the summed counts data (fDat), and optionally, the experimental data (cDat)

RGLab/RNASeqPipelineR documentation built on Jan. 19, 2020, 12:31 a.m.