ASEset-gviztrack: ASEset-gviztrack ASEset objects

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description

plotting ASE effects over a specific genomic region

Usage

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,
  ...
)

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.

Author(s)

Jesper R. Gadin

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')

pappewaio/AllelicImbalance documentation built on April 11, 2020, 2:58 a.m.