Description Usage Arguments Details Author(s) Examples
Create a hub or session track line txt file for bigWig files. The txt file is stored at current location.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | 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$",
shortLabel=NULL,
longLabel=NULL)
|
bwDir |
The location of the bigWig files. At Tapscott Lab, the bigWig file (.bw) should be placed at '/fh/fast/tapscott_s/pub/tapscott/ucsc/bigWig/your_project'. The junction bigBed files (.bb) should be placed at '/fh/fast/tapscott_s/pub/tapscott/ucsc/junctions/your_project'. |
projectName |
The sub-directory in /home/tapscott/ucsc/bigWig where the bigWig files are stored or /home/tapscott/ucsc/junctions where the bigBed files are stored. |
trackName |
A character indicating the parent track attributes appears on the Hub. It should not have empty space. |
TrackFileName |
A character string indicating the name of the hub track file. If NULL, a txt file named "$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. |
The bigWig files must be placed at '/fh/fast/tapscott_s/pub/tapscott/ucsc/bigWig/your_project'.
Chao-Jen Wong <cwon2@fhcrc.org>
1 2 3 4 5 6 7 8 9 10 | ## 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")
|
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