createSignalTracks {metaseqR2} | R Documentation |
This function creates bigWig files to be used for exploring RNA signal in genome browsers. When strands are separated, a UCSC genome browser trackhub is created to group tracks for the same sample. A link to the created data is returned.
createSignalTracks(targets, org, urlBase = NULL, stranded = FALSE, normTo = 1e+9, exportPath = ".", hubInfo = list(name = "MyHub", shortLabel = "My hub", longLabel = "My hub", email = "someone@example.com"), fasta = NULL, gtf = NULL, forceHub = FALSE, overwrite = FALSE, rc = NULL)
targets |
a tab-delimited file with the experimental
description or the output of |
org |
See the |
urlBase |
a valid URL which is prepended to the created bigWig files. |
stranded |
Separate + and - strands and create separate bigWig files. |
normTo |
the total sum of signal to be used as the
normalization target. See also the |
exportPath |
path to export tracks. |
hubInfo |
information regarding the track hub created
when |
overwrite |
overwrite tracks if they exist? Defaults to
|
fasta |
reference genome in FASTA format for the case of analyzing a custom, non-directly supported organism. It will be converted to the .2bit format and written along with a track hub. |
gtf |
a GTF file describing gene models in the case of analyzing a custom, non-directly supported organism. It will be converted to the .bigBed format and written along with a track hub. |
forceHub |
when |
rc |
Fraction of cores to use. |
A string with the link(s) to the created tracks.
Panagiotis Moulos
dataPath <- system.file("extdata",package="metaseqR2") targets <- data.frame(samplename=c("C","T"), filename=file.path(dataPath,c("C.bam","T.bam")), condition=c("Control","Treatment"), paired=c("single","single"),stranded=c("forward","forward")) path <- tempdir() write.table(targets,file=file.path(path,"targets.txt"), sep="\t",row.names=FALSE,quote=FALSE) if (.Platform$OS.type == "unix") link <- createSignalTracks(file.path(path,"targets.txt"),"mm9")