coverageRate {InPAS}R Documentation

coverage rate of genes and 3UTRs

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)))
    }

[Package InPAS version 1.16.3 Index]