ASEset-gviztrack {AllelicImbalance} | R Documentation |
plotting ASE effects over a specific genomic region
ASEDAnnotationTrack(x, GR = rowRanges(x), type = "fraction", strand = "*", trackName = paste("deTrack", type), verbose = TRUE, ...) ## S4 method for signature 'ASEset' 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, ...)
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 |
... |
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) |
For information of how to use these tracks in more ways, visit the Gviz package manual.
Jesper R. Gadin
The ASEset
class which the functions
can be called up on.
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')