usage4plot {InPAS}R Documentation

prepare coverage data and fitting data for plot

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)

[Package InPAS version 1.16.2 Index]