createSessionTrackLine: Create UCSC Genome Browser Session Track Line

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

Description

Create a session track line txt file

Usage

createSessionTrackLine.BW(projectName, sessionFileName = NULL,
                       type = "bigWig", sample.group,
		       pattern="\.bw$", group.col = NULL,
		       brewer = "Set2")

Arguments

projectName	The sub-directory in /home/tapscott/ucsc/bigWig where the bigWig files are stored.
sessionFileName	A character string indicating the name of the session track file. If NULL, a txt file named "sessionTrackLines.txt" is created and saved in the current directory.
type	"bigWig".
sample.group	A factor indicating the sample grouping and the color of the track will be assigned accordingly.
pattern	An optional regular expression. Only file names which match the regular expression will be returned. The default if the file names end up with .bw.
group.col	A character string indicating the color for the track. If "NULL", the color patette is signed by the brewer arguement.
brewer	A character string indicating the name of palette. See RColorBrewer's brewer.pal function.

Details

The bigWig files must be placed in /home/tapscott/ucsc/bigWig.

Author(s)

Chao-Jen Wong <[e-mail]>

Examples

## Not run: 
setwd("/home/tapscott/ucsc/bigWig/hg19_Dux4_RD_inducible")
getwd()
createSessionTrackLine.BW(projectName="hg19_Dux4_RD_inducible", sample.group=c(1,2))

## End(Not run)

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