usage4plot {InPAS} | R Documentation |
prepare coverage data and fitting data for plot
usage4plot(gr, coverage, proximalSites, genome, groupList)
gr |
an object of GRanges |
coverage |
coverage for each sample |
proximalSites |
proximal sites |
genome |
an object of BSgenome |
groupList |
the list of sample names |
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 |
Jianhong Ou
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)