coverageRate: coverage rate of genes and 3UTRs

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Description

calculate coverage rate of gene and 3UTRs. This function is used for quality control of the coverage. The coverage rate can show the complexity of RNA-seq library.

Usage

    coverageRate(coverage, txdb, genome, 
                         cutoff_readsNum=1,
                         cutoff_expdGene_cvgRate=0.1,
                         cutoff_expdGene_sampleRate=0.5,
                         which=NULL, ...)

Arguments

coverage	coverage for each sample, output of coverageFromBedGraph
txdb	an object of TxDb
genome	an object of BSgenome
cutoff_readsNum	cutoff reads number. If the coverage in the location is greater than cutoff_readsNum, the location will be treated as coveraged by signal.
cutoff_expdGene_cvgRate,cutoff_expdGene_sampleRate	cutoff_expdGene_cvgRate and cutoff_expdGene_sampleRate are the parameters used to calculate which gene is expressed in all input dataset. cutoff_expdGene_cvgRate set the cutoff value for the coverage rate of each gene; cutoff_expdGene_sampleRate set the cutoff value for ratio of numbers of expressed and all samples for each gene. for example, by default, cutoff_expdGene_cvgRate=0.1 and cutoff_expdGene_sampleRate=0.5, surppose there are 4 samples, for one gene, if the coverage rates by base are: 0.05, 0.12, 0.2, 0.17, this gene will be count as expressed gene because mean(c(0.05, 0.12, 0.2, 0.17) > cutoff_expdGene_cvgRate) > cutoff_expdGene_sampleRate if the coverage rates by base are: 0.05, 0.12, 0.07, 0.17, this gene will be count as un-expressed gene because mean(c(0.05, 0.12, 0.07, 0.17) > cutoff_expdGene_cvgRate) <= cutoff_expdGene_sampleRate
which	an object of GRanges or NULL. If it is not NULL, only the exons overlapping the given ranges are used.
...	not used.

Value

return a datafrom with colnames : gene.coverage.rate: coverage per base for all genes, expressed.gene.coverage.rate: coverage per base for expressed genes, UTR3.coverage.rate: coverage per base for all 3' UTRs, UTR3.expressed.gene.subset.coverage.rate: coverage per base for 3' UTRs of expressed genes. and rownames: the names of coverage.

Author(s)

Jianhong Ou

Examples

    if(interactive()){
        library(BSgenome.Mmusculus.UCSC.mm10)
        library(TxDb.Mmusculus.UCSC.mm10.knownGene)
        path <- file.path(find.package("InPAS"), "extdata")
        bedgraphs <- c(file.path(path, "Baf3.extract.bedgraph"), 
                        file.path(path, "UM15.extract.bedgraph"))
        hugeData <- FALSE
        
        coverage <- coverageFromBedGraph(bedgraphs, 
                                 tags=c("Baf3", "UM15"),
                                 genome=BSgenome.Mmusculus.UCSC.mm10,
                                 hugeData=hugeData)
        coverageRate(coverage,
                    txdb=TxDb.Mmusculus.UCSC.mm10.knownGene,  
                    genome=BSgenome.Mmusculus.UCSC.mm10,
                    which = GRanges("chr6", ranges=IRanges(98013000, 140678000)))
    }

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.