ASEset-gviztrack {AllelicImbalance} | R Documentation

## ASEset-gviztrack ASEset objects

### 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')

[Package AllelicImbalance version 1.22.0 Index]