ASEset-glocationplot: glocationplot ASEset objects

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description

plotting ASE effects over a specific genomic region using Gviz functionality

Usage

glocationplot(
  x,
  type = "fraction",
  strand = "*",
  BamGAL = NULL,
  GenomeAxisTrack = FALSE,
  trackNameDeAn = paste("deTrack", type),
  TxDb = NULL,
  sizes = NULL,
  add = FALSE,
  verbose = FALSE,
  ...
)

Arguments

x	an ASEset object.
type	'fraction' or 'count'
strand	'+','-','*' or 'both'. This argument determines which strand is plotted. See getAlleleCounts for more information of choice of strand.
BamGAL	GAlignmentsList covering the same genomic region as the ASEset
GenomeAxisTrack	include an genomic axis track
trackNameDeAn	trackname for deAnnotation track
TxDb	a TxDb object which provides annotation
sizes	vector with the sum 1. Describes the size of the tracks
add	add to existing plot
verbose	if set to TRUE it makes function more talkative
...	arguments passed on to barplot function

Details

The glocationplot methods visualises the distribution of ASE over a larger region on one chromosome. It takes and ASEset object as well as additional information on plot type (see gbarplot), strand type (see getAlleleCounts), Annotation tracks are created from the Gviz packageh. It is obviously important to make sure that the genome build used is set correctly, e.g. 'hg19'.

sizes has to be of the same length as the number of tracks used.

Author(s)

Jesper R. Gadin

See Also

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

Examples

data(ASEset)
genome(ASEset) <- 'hg19'

glocationplot(ASEset,strand='+')

#for ASEsets with fewer SNPs the 'count' type plot is useful 
glocationplot(ASEset,type='count',strand='+')

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