createHubTrackLine: Create UCSC Genome Browser Hub Track Line Attributes for...

In TapscottLab/UCSCTrackTools: Tools to convert BAM files to BigWig and to create session track line

Description

Create a hub or session track line txt file for bigWig files. The txt file is stored at current location.

Usage

    createSessionTrackLine.BW(projectName,
                              trackName=NULL,
                              TrackFileName = NULL,
                              col = c(102, 194, 165),
                              pattern=".bw$",
			      shortLabel=NULL,
			      longLabel=NULL)
			      
    createHubTrackLine.BW(bwDir,
	                  trackName,
                          TrackFileName = NULL,
                          col = c(102, 194, 165),
                          pattern=".bw$",
			  shortLabel=NULL,
			  longLabel=NULL)
			  
    createHubTrackLine.junc.bed(projectName,
                                trackName=NULL,
                                TrackFileName = NULL,
                                col = c(102, 194, 165),
                                pattern=".bd$",
			        shortLabel=NULL,
			        longLabel=NULL)
				

Arguments

bwDir	The location of the bigWig files. At Tapscott Lab, the bigWig file (.bw) should be placed at '/fh/fast/tapscott_s/pub/tapscott/ucsc/bigWig/your_project'. The junction bigBed files (.bb) should be placed at '/fh/fast/tapscott_s/pub/tapscott/ucsc/junctions/your_project'.
projectName	The sub-directory in /home/tapscott/ucsc/bigWig where the bigWig files are stored or /home/tapscott/ucsc/junctions where the bigBed files are stored.
trackName	A character indicating the parent track attributes appears on the Hub. It should not have empty space.
TrackFileName	A character string indicating the name of the hub track file. If NULL, a txt file named "$projectName__HubTrackLines.txt" is created and saved in the current directory.
col	Color default to RGB:c(102, 194, 165)
pattern	A character indicating the pattern of the bigWig file extension.
shortLabel	A character indicating the shortLabel attribute for the track lines.
longLabel	A character indicating the longLabel attribute for the track lines.

Details

The bigWig files must be placed at '/fh/fast/tapscott_s/pub/tapscott/ucsc/bigWig/your_project'.

Author(s)

Chao-Jen Wong <[e-mail]>

Examples

## this ucscDir is where the Tapscott Lab stores the bigWig files for the Hub
ucscDir <-  "/fh/fast/tapscott_s/pub/tapscott/ucsc/bigWig"
## define the sub-directory
bwDir <- file.path(ucscDir, "hg19_Dux4_RD_inducible")
library(RColorBrewer)
col <- col2rgb(brewer.pal(3, "Set2"))
createHubTrackLine.BW(bwDir=bwDir,
                      trackName="Dux4_RD_inducible",
     		      col=col[, 2],
		      longLabel="Dux4_RD_inducible RNA-Seq Coverage")

TapscottLab/UCSCTrackTools documentation built on May 16, 2019, 2:28 a.m.