RIPSeeker (version 1.12.0)

viewRIP:

Visualize peaks from UCSC genome browser.

Description

Upload alignments, peaks, statistical scores to UCSC genome browser for comparative visualization of the results and data available in the UCSC database.

Usage

viewRIP(seekedRIP, alignGR, alignGRCTL, 
	binGR = seekedRIP, scoreType = "eFDR", 
	cutoffLine = 0.001, displayALLChr = FALSE, ...)

Arguments

seekedRIP

GRangesList obtained from ripSeek. Each list item represents the RIP peaks on a chromosome accompanied with statistical scores including (read) count, logOddScore, pval, pvalAdj, eFDR for the RIP and control (if available). Please refer to seekRIP for more details.

alignGR

GRanges of read alignments for the RIP.

alignGRCTL

GRanges of read alignments for the control.

binGR

GRanges containing read count column corresponding to the peaks. By default, alignGR is used as binGR to display the read count in RIP condition.

scoreType

Type of statistical score to display as another track in the browser (Default: eFDR). eFDR/pval/pvalAdj is displayed at -log10 scale.

cutoffLine

Draw a cutoffline in the browser to indicate the significance level above which the peaks are considered significant.

displayALLChr

Binary indicator when TRUE upload and display the information for only one chromosome rather than upload all chromosomes (Default: TRUE).

...

Extra arguments are ignored.

Details

The function is a wrapper function of browserSession, track, and browserView.

References

Michael Lawrence, Vince Carey and Robert Gentleman (). rtracklayer: R interface to genome browsers and their annotation tracks. R package version 1.16.3.

See Also

ripSeek, browserSession, track, browserView

Examples

if(interactive()) { # need internet connection
# Retrieve system files
extdata.dir <- system.file("extdata", package="RIPSeeker") 

bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)

bamFiles <- grep("PRC2", bamFiles, value=TRUE)

cNAME <- "SRR039214" 						# specify control name


# Parameters setting
binSize <- NULL							# automatically determine bin size
minBinSize <- 10000						# min bin size in automatic bin size selection
maxBinSize <- 12000						# max bin size in automatic bin size selection
multicore <- TRUE						# use multicore
strandType <- "-"						# set strand type to minus strand


################ run main function ripSeek to predict RIP ################
seekOut <- ripSeek(bamPath=bamFiles, cNAME=cNAME, 
		binSize=binSize, minBinSize = minBinSize, 
		maxBinSize = maxBinSize, strandType=strandType, 
		silentMain=TRUE, verbose=FALSE, 
		reverseComplement=TRUE, genomeBuild="mm9",
		uniqueHit = TRUE, assignMultihits = TRUE, 
		rerunWithDisambiguatedMultihits = TRUE, multicore=multicore)


################ visualization ################

viewRIP(seekOut$RIPGRList$chrX, seekOut$mainSeekOutputRIP$alignGalFiltered, 
	seekOut$mainSeekOutputCTL$alignGalFiltered, scoreType="eFDR")
}