AllelicImbalance (version 1.10.2)

ASEset-glocationplot: glocationplot ASEset objects

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.

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='+')