ASEset-glocationplot {AllelicImbalance} | R Documentation

## 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.

### 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='+')

[Package AllelicImbalance version 1.20.0 Index]