getUTR3eSet {InPAS} | R Documentation |
Generate a UTR3eSet object with PDUI infomation for statistic test
getUTR3eSet(CPsites, coverage, genome, utr3, normalize=c("none", "quantiles", "quantiles.robust", "mean", "median"), ..., BPPARAM=NULL, singleSample=FALSE)
CPsites |
outputs of CPsites |
coverage |
coverage for each sample, outputs of coverageFromBedGraph |
genome |
an object of BSgenome |
utr3 |
output of utr3Annotation |
normalize |
normalization method |
... |
parameter can be passed into normalize.quantiles.robust |
BPPARAM |
An optional |
singleSample |
prepare data for singleSample analysis? default is FALSE |
An object of UTR3eSet which contains following elements:
usage: an GRanges object with CP sites info.
PDUI: a matrix of PDUI
PDUI.log2: log2 transformed PDUI matrix
short: a matrix of usage of short form
long: a matrix of usage of long form
if singleSample is TRUE, one more element, signals, will be included.
Jianhong Ou
path <- file.path(find.package("InPAS"), "extdata") load(file.path(path, "CPs.MAQC.rda")) load(file.path(path, "coverage.MAQC.rda")) library(BSgenome.Hsapiens.UCSC.hg19) data(utr3.hg19) getUTR3eSet(CPsites=CPs, coverage=coverage, genome=BSgenome.Hsapiens.UCSC.hg19, utr3=utr3.hg19)