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 1.20.0 Index]