wavClusteR (version 2.6.2)

getMetaTSS: 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.

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 )
tss <- getMetaTSS( sortedBam = example )