UCSCStyle: UCSCStyle

In CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

Description

Set the style of the chromosome names to UCSC ("chr1" instead of "1")

Usage

UCSCStyle(x)

Arguments

x	(GRanges, GRangesList or list of GRanges) The object to transform to UCSC style

Value

The same x object with the styles of the seqlevels set to UCSC

Examples

#GRanges
seg.data <- regioneR::toGRanges(data.frame(chr = c("1", "1", "2", "5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(NA,0.25,1.5,NA)))
seg.data <- UCSCStyle(seg.data)

#List of GRanges
seg.data <- list(a = regioneR::toGRanges(data.frame(chr = c("1", "1", "2", "5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(NA,0.25,1.5,NA),baf = c(1.5,2.5,NA,6), id = c("rs52456","rs52457","rs52458","rs52459"))),
                    b=regioneR::toGRanges(data.frame(chr = c("1", "1", "2", "5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(2.5,NA,1.5,0.25), baf = c(1.5,2.5,NA,6), id = c("rs52456","rs52457","rs52458","rs52459"))))
seg.data <- UCSCStyle(seg.data)

#GRangesList
seg.data <- GRangesList(a = regioneR::toGRanges(data.frame(chr = c("1", "1", "2", "5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(NA,0.25,1.5,NA), baf = c(1.5,2.5,NA,6), id = c("rs52456","rs52457","rs52458","rs52459"))),
                        b = regioneR::toGRanges(data.frame(chr = c("1", "1", "2", "5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(2.5,NA,1.5,0.25), baf = c(1.5,2.5,NA,6), id = c("rs52456","rs52457","rs52458","rs52459"))))
seg.data <- UCSCStyle(seg.data)

CopyNumberPlots documentation built on Nov. 8, 2020, 6:51 p.m.