spViewPerFeature {ShortRead} | R Documentation

## Tools to visualize genomic data

### Description

Use `Snapshot`-class to visualize a specific region of genomic data

### Usage

    spViewPerFeature(GRL, name, files, ignore.strand=FALSE,
                     multi.levels = FALSE, fac=character(0L), ...)

### Arguments

`GRL` | Object `GRangeList` containing annotation of genomic data. It can be generated by applying `exonsBy()` or `transcriptsBy()` to a `TxDb` instance. See examples below.
`name` | Character(1) specifying which element in `GRL` to be visualized.
`files` | Charactor() or `BamFileList` specifying the file(s) to be visualized. If multiple files, local metadata of the files can be hold by setting a `DataFrame` (values(files) <- DataFrame(...)). See examples below.
`ignore.strand` | Logical(1) indicating whether to ignore the strand of the genomic data.
`multi.levels` | Logical(1) indicating whether to plot the coverage of multiple files on different panels. If `FALSE`, the mean coverage of multiple files would be plotted.
`fac` | Character(1) indicating which column of local metadata (`elementMetatdata()`) should be used to group the samples. Ignore
`...` | Arguments used for creating a `Snapshot` object.

### Value

A `Snapshot` instance

### Author(s)

Chao-Jen Wong cwon2@fhcrc.org

### See Also

`Snapshot`

### Examples

    ## Example 1
    library(GenomicFeatures)
    txdbFile <- system.file("extdata", "sacCer2_sgdGene.sqlite",
                             package="yeastNagalakshmi")

    ## either use a txdb file quaried from UCSC or use existing TxDb packages.
    txdb <- loadDb(txdbFile)

    grl <- exonsBy(txdb, by="gene")
    file <- system.file("extdata", "SRR002051.chrI-V.bam",
                             package="yeastNagalakshmi")
    s <- spViewPerFeature(GRL=grl, name="YAL001C", files=file)

    ## Example 2
    ## multi-files: using 'BamFileList' and setting up the 'DataFrame'
    ## holding the phenotype data

    bfiles <- BamFileList(c(a=file, b=file))
    values(bfiles) <- DataFrame(sampleGroup=factor(c("normal", "tumor")))
    values(bfiles)

    s <- spViewPerFeature(GRL=grl, name="YAL001C",
                          files=bfiles, multi.levels=TRUE, fac="sampleGroup")

[Package ShortRead version 1.45.4 Index]