getMetaTSS {wavClusteR} | R Documentation

## Compute and plot read densities in genomic regions around transcription start sites

### Description

Aligned reads are used generate a metaTSS profile across genomic regions containing transcription start sites (TSSs).

### Usage

    getMetaTSS(sortedBam, txDB = NULL, upstream = 1e3, downstream = 1e3,
    nBins = 40, genome = 'hg19', tablename = 'ensGene', unique = FALSE, plot =
    TRUE, verbose = TRUE, ...)

### Arguments

`sortedBam` | GRanges object containing aligned reads as returned by readSortedBam
`txDB` | TranscriptDb object obtained through a call to the `makeTxDbFromUCSC` function in the `GenomicFeatures` package. Default is NULL, namely the object will be fetched internally
`upstream` | An integer corresponding to the number of bases to be considered upstream the TSS. Default is 1000
`downstream` | An integer corresponding to the number of bases to be considered downstream the TSS. Default is 1000
`nBins` | An integer corresponding to the number of bins to be used to partition the genes. Default is 40, i.e. bin size 50 bases
`genome` | A character specifying the genome abbreviation used by UCSC. Available abbreviations are returned by a call to `ucscGenomes()[ , "db"]`. Default is "hg19" (human genome)
`tablename` | A character specifying the name of the UCSC table containing the transcript annotations to retrieve. Available table names are returned by a call to `supportedUCSCtables()`. Default is "ensGene", namely ensembl gene annotations
`unique` | Logical, if TRUE only non-overlapping TSSs extended by upstream/downstream are considered. Default is FALSE, i.e. all TSSs are considered
`plot` | Logical, if TRUE a dotchart with cluster annotations is produced
`verbose` | Logical, if TRUE processing steps are printed
`...` | Additional parameters to be passed to the `plot` function

### Value

A numeric vector of the same length as `nBins` containing normalized counts. If `plot`, the metaTSS profile is also depicted as a line plot.

### Author(s)

Federico Comoglio

### References

Comoglio F*, Sievers C* and Paro R, wavClusteR: an R package for PAR-CLIP data analysis, submitted

### See Also

`readSortedBam`

### Examples

    require(BSgenome.Hsapiens.UCSC.hg19)

    filename <- system.file( "extdata", "example.bam", package = "wavClusteR" )
    example <- readSortedBam( filename = filename )
    ## Not run: tss <- getMetaTSS( sortedBam = example )

[Package wavClusteR version 2.12.1 Index]