usage4plot: prepare coverage data and fitting data for plot

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

Description

prepare coverage data and fitting data for plot

Usage

    usage4plot(gr, coverage, proximalSites, genome, groupList)

Arguments

gr	an object of GRanges
coverage	coverage for each sample
proximalSites	proximal sites
genome	an object of BSgenome
groupList	the list of sample names

Value

Formal class 'GRanges' [package "GenomicRanges"] with metadata:

dat	matrix, first column is the fit data, the other columns are coverage data for each sample
offset	offset from the start of 3UTR

Author(s)

Jianhong Ou

Examples

    library(BSgenome.Mmusculus.UCSC.mm10)
    path <- file.path(find.package("InPAS"), "extdata")
    bedgraphs <- c(file.path(path, "Baf3.extract.bedgraph"), 
               file.path(path, "UM15.extract.bedgraph"))
    coverage <- coverageFromBedGraph(bedgraphs, tags=c("Baf3", "UM15"), 
                                genome=Mmusculus, hugeData=FALSE)
    gr <- GRanges("chr6", IRanges(128846245, 128850081), strand="-")
    dat <- usage4plot(gr, coverage, proximalSites=128849148, Mmusculus)
    data <- dat$dat[[1]]
    op <- par(mfrow=c(3, 1))
    plot(data[,1], type="l", xlab="", ylab="The fitted value")
    abline(v=dat$offset)
    plot(data[,2], type="l", xlab="", ylab="Baf3")
    plot(data[,3], type="l", xlab="", ylab="UM15")
    par(op)

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