viewRIP {RIPSeeker} | R Documentation |
Upload alignments, peaks, statistical scores to UCSC genome browser for comparative visualization of the results and data available in the UCSC database.
viewRIP(seekedRIP, alignGR, alignGRCTL, binGR = seekedRIP, scoreType = "eFDR", cutoffLine = 0.001, displayALLChr = FALSE, ...)
seekedRIP |
|
alignGR |
|
alignGRCTL |
|
binGR |
|
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. |
The function is a wrapper function of browserSession
, track
, and browserView
.
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.
Yue Li
Michael Lawrence, Vince Carey and Robert Gentleman (). rtracklayer: R interface to genome browsers and their annotation tracks. R package version 1.16.3.
ripSeek, browserSession, track, browserView
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") }