generateCoverageDF_contigs: Generate coverage data frame for specific candidates

Description Usage Arguments Value

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

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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.