AllelicImbalance (version 1.10.2)

ASEset-gviztrack: ASEset-gviztrack ASEset objects

Description

plotting ASE effects over a specific genomic region

Usage

ASEDAnnotationTrack(x, GR = rowRanges(x), type = "fraction", strand = "*", trackName = paste("deTrack", type), verbose = TRUE, ...)
"ASEDAnnotationTrack"(x, GR = rowRanges(x), type = "fraction", strand = "*", trackName = paste("deTrack", type), verbose = TRUE, ...)
CoverageDataTrack(x, GR = rowRanges(x), BamList = NULL, strand = NULL, start = NULL, end = NULL, trackNameVec = NULL, meanCoverage = FALSE, verbose = TRUE, ...)

Arguments

x

an ASEset object.

GR

genomic range of plotting

type

'fraction' or 'count'

strand

'+','-'. This argument determines which strand is plotted.

trackName

name of track (ASEDAnnotationTrack)

verbose

Setting verbose=TRUE gives details of procedure during function run

...

arguments passed on to barplot function

BamList

GAlignmnentsList object of reads from the same genomic region as the ASEset

start

start position of reads to be plotted

end

end position of reads to be plotted

trackNameVec

names of tracks (CoverageDataTrack)

meanCoverage

mean of coverage over samples (CoverageGataTrack)

Details

For information of how to use these tracks in more ways, visit the Gviz package manual.

See Also

• The ASEset class which the functions can be called up on.

Examples

data(ASEset)
x <- ASEset[,1:2]
r <- reads[1:2]
genome(x) <- 'hg19'
seqlevels(r) <- seqlevels(x)

GR <- GRanges(seqnames=seqlevels(x),
		ranges=IRanges(start=min(start(x)),end=max(end(x))),
		strand='+', genome=genome(x))

deTrack <- ASEDAnnotationTrack(x, GR=GR, type='fraction',strand='+')
covTracks <- CoverageDataTrack(x,BamList=r,strand='+') 

lst <- c(deTrack,covTracks)

sizes <- c(0.5,rep(0.5/length(covTracks),length(covTracks)))
#temporarily do not run this function 
#plotTracks(lst, from=min(start(x)), to=max(end(x)), 
#sizes=sizes, col.line = NULL, showId = FALSE, main='mainText', 
#cex.main=1, title.width=1, type='histogram')