R: Visualize peaks from UCSC genome browser.

viewRIP {RIPSeeker}

R Documentation

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.

Note

If input contain multiple chromosomes, then multiple browser window will be open to display each chromosome. A more user-friendly way is to upload all of the information to UCSC and open a single browser for visualization, which may become one of the new features in future release.

Author(s)

Yue Li

References

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

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")
}

[Package RIPSeeker version 1.20.0 Index]