Description Usage Arguments Value Author(s) Examples
prepare coverage data and fitting data for plot
1 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | 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)
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