getMetaGene: Compute and plot metagene profile using identified clusters

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

Description

Transcriptome-wide identified clusters are used to generate a metagene profile by binning gene bodies, upstream and downstream regions.

Usage

getMetaGene(clusters, txDB = NULL, upstream = 1e3, downstream = 1e3,
nBins = 40, nBinsUD = 10, minLength = 1, genome = 'hg19', tablename =
'ensGene', plot = TRUE, verbose = TRUE, ...)

Arguments

clusters	GRanges object containing individual clusters as identified by the getClusters function
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 gene. Default is 1000
downstream	An integer corresponding to the number of bases to be considered downstream the gene. Default is 1000
nBins	An integer corresponding to the number of bins to be used to partition the genes. Default is 40
nBinsUD	An integer corresponding to the number of bins to be used to partion upstream and downstream regions. Defauls is 10, i.e. the bin size is 100 bases for the default extension
minLength	An integer indicating the the minimum required length of a gene in order for it to be considered. Default is 1, i.e. all genes are considered
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
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 + 2 * nBinsUD containing normalized counts. If plot, the metagene profile is also depicted as a line plot.

Author(s)

Federico Comoglio

Comoglio F, Sievers C and Paro R (2015) Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data, BMC Bioinformatics 16, 32.

References

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

See Also

getClusters

Examples

require(BSgenome.Hsapiens.UCSC.hg19)

data( model, package = "wavClusteR" ) 

filename <- system.file( "extdata", "example.bam", package = "wavClusteR" )
example <- readSortedBam( filename = filename )
countTable <- getAllSub( example, minCov = 10, cores = 1 )
highConfSub <- getHighConfSub( countTable, supportStart = 0.2, supportEnd = 0.7, substitution = "TC" )
coverage <- coverage( example )
clusters <- getClusters( highConfSub = highConfSub, 
                         coverage = coverage, 
                         sortedBam = example, 
	                 threshold = 2 ) 

fclusters <- filterClusters( clusters = clusters, 
		             highConfSub = highConfSub, 
        		     coverage = coverage,
			     model = model, 
			     genome = Hsapiens, 
		             refBase = 'T', 
		             minWidth = 12 )
## Not run: meta <- getMetaGene( clusters = fclusters )

FedericoComoglio/wavClusteR documentation built on Oct. 29, 2020, 2:44 p.m.