generateCoverageDF_contigs: Generate coverage data frame for specific candidates

In SimonSchafferer/RNASeqUtility: ncRNA RNA-Seq analysis utilities

Description

This method returns a data frame containing coverage values for each position. It is intended for genome mapping results. For ncRNA mappings please see: generateCoverageDF_ncRNAmappings

Usage

generateCoverageDF_contigs(contigsGR, contigResTable, bedgraphMapping_plusL,
  bedgraphMapping_minusL, sampleNames, annotationGR)

Arguments

contigsGR	GRanges file containing the coordinates of the contigs and their contigID (specified as contigID in the metadata)
contigResTable	Selected candidates from the result of differential expression analysis from DESeq2 combined with the minimum annotation dataframe
bedgraphMapping_plusL	the cmdResult object of the bedgraph plus mapping (genomeCovNcRNAMapping_plusL)
bedgraphMapping_minusL	the cmdResult object of the bedgraph minus mapping (genomeCovNcRNAMapping_minusL)
sampleNames	names of the samples from samplesInfo table
annotationGR	An otpional annotation GRanges object, when provided the annotation will be used as reference interval

Value

data.frame containing the read counts for each position in order to create a histogram of read counts for each ncRNA

SimonSchafferer/RNASeqUtility documentation built on May 9, 2019, 1:34 p.m.