getMetaTSS: Compute and plot read densities in genomic regions around...

In wavClusteR: Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

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 )

wavClusteR documentation built on Nov. 8, 2020, 6:54 p.m.