Description Usage Arguments Details Author(s) See Also Examples
A wrapper calls up three major functions to create junction bed file, junction tracks bigBed files, and generate a track line files specifying the attribute of the junciton track.
1 2 3 4 5 | makeJunctionTracksWrapper(bamFiles, genome, cores = 1L,
seqlev = NULL, min_junction_count = 2,
bedDir = ".", juncDir = ".",
chrom_sizefile,
trackName)
|
bamFiles |
character strings of the bam files. |
genome |
a character string specifying the genome of the subject. |
cores |
an integer indicating the number of cores. |
seqlev |
character strings specifying the sequence levels desired to be included in the junction files. |
min_junction_count |
an integer specifying the minimal number of junction read. |
bedDir |
a character string indicating the destination of the junction bed (.bed) files. |
juncDir |
a character string indicating the destination of the junction bigBed (.bb) files. The preferred location is "/fh/fast/tapscott_s/pub/tapscott/ucsc/junctions/...". |
chrom_sizefile |
a file name of the chromozon size file pertained to the genome. Those files can be found in "/fh/fast/tapscott_s/CompBio/hg38, /mm10, and /canFam3". |
trackName |
a character string specifying the name of the track to be appeared on UCSC genome browser. |
The wrapper calls three functions: makeJunctionBed(), convertBedToBigBed(), and createHubTrackLine.junc.bed(). See example below.
Chao-Jen Wong <cwon2@fhcrc.org>
makeJunctionBed
, createHubTrackLine.junc.bed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | ## Not run:
pkgDir <- "/fh/fast/tapscott_s/R/RNA-Seq/canFam3.DuxFamily"
load(file.path(pkgDir, "data", "canine.ens.SE.rda"))
ucscDir <- "/fh/fast/tapscott_s/pub/tapscott/ucsc/junctions"
ngsDir <- "/shared/ngs/illumina/atyler/170208_SN367_0857_AHF37NBCXY"
## define parameters
bamDir <- file.path(ngsDir, "tophat", "bam")
bamFiles <- list.files(bamDir, pattern="\.bam$",
full.names=TRUE)[c(1,5, 6)]
seqlev <- seqlevels(canine.ens.SE)
chrom_sizefile <- "/fh/fast/tapscott_s/CompBio/canFam3/canFam3.chrom.sizes"
bedDir <- file.path(pkgDir, "inst", "junction_bed")
## bigBedDir is the location where files for the Hub reside.
bigBedDir <- file.path(ucscDir, "canFam3_CnMb_luciferase")
trackName <- "CnMb_luciferase_junc"
makeJunctionTracksWrapper(bamFiles, genome="canFam3",
cores=1L, seqlev=seqlev,
min_junction_count=2,
chrom_sizefile=chrom_sizefile,
bedDir=bedDir,
bigBedDir=bigBedDir,
trackName=trackName)
## End(Not run)
|
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