InPAS (version 1.4.4)

usage4plot: prepare coverage data and fitting data for plot

Description

prepare coverage data and fitting data for plot

Usage

usage4plot(gr, coverage, proximalSites, genome, groupList,  gcCompensation=NA, mappabilityCompensation=NA,  FFT=FALSE, fft.sm.power=20)

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

gcCompensation

GC content compensation vector

mappabilityCompensation

mappability compensation vector

FFT

use FFT to smooth the data or not. default: FALSE

fft.sm.power

if FFT is TRUE, the frequency should be removed

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

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)