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

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='+')

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(AllelicImbalance)
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AllelicImbalance/ASEset-glocationplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ASEset-glocationplot
> ### Title: glocationplot ASEset objects
> ### Aliases: ASEset-glocationplot glocationplot glocationplot,ASEset-method
> ### Keywords: glocationplot
> 
> ### ** 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='+')
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>