getMetaTSS {wavClusteR} | R Documentation |
Aligned reads are used generate a metaTSS profile across genomic regions containing transcription start sites (TSSs).
getMetaTSS(sortedBam, txDB = NULL, upstream = 1e3, downstream = 1e3, nBins = 40, genome = 'hg19', tablename = 'ensGene', unique = FALSE, plot = TRUE, verbose = TRUE, ...)
sortedBam |
GRanges object containing aligned reads as returned by readSortedBam |
txDB |
TranscriptDb object obtained through a call to the
|
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 |
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 |
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 |
A numeric vector of the same length as nBins
containing
normalized counts. If plot
, the metaTSS profile is also depicted as a
line plot.
Federico Comoglio
Comoglio F*, Sievers C* and Paro R, wavClusteR: an R package for PAR-CLIP data analysis, submitted
require(BSgenome.Hsapiens.UCSC.hg19) filename <- system.file( "extdata", "example.bam", package = "wavClusteR" ) example <- readSortedBam( filename = filename ) ## Not run: tss <- getMetaTSS( sortedBam = example )