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.

### 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")
    }

[Package RIPSeeker version 1.20.0 Index]