Description Usage Arguments Value Author(s) See Also Examples
View source: R/expressed_regions.R
This function uses the pre-computed mean coverage for a given SRA project to identify the expressed regions (ERs) for a given chromosome. It returns a GRanges-class object with the expressed regions as defined by findRegions.
1 2 3 4 5 6 7 8 9 10 | expressed_regions(
project,
chr,
cutoff,
outdir = NULL,
maxClusterGap = 300L,
chrlen = NULL,
verbose = TRUE,
...
)
|
project |
A character vector with one SRA study id. |
chr |
A character vector with the name of the chromosome. |
cutoff |
The base-pair level cutoff to use. |
outdir |
The destination directory for the downloaded file(s) that were
previously downloaded with download_study. If the files are missing,
but |
maxClusterGap |
This determines the maximum gap between candidate ERs. |
chrlen |
The chromosome length in base pairs. If it's |
verbose |
If |
... |
Additional arguments passed to download_study when
|
A GRanges-class object as created by findRegions.
Leonardo Collado-Torres
download_study, findRegions, railMatrix
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Define expressed regions for study SRP009615, chrY
if (.Platform$OS.type != "windows") {
## Reading BigWig files is not supported by rtracklayer on Windows
regions <- expressed_regions("SRP009615", "chrY",
cutoff = 5L,
maxClusterGap = 3000L
)
}
## Not run:
## Define the regions for multiple chrs
regs <- sapply(chrs, expressed_regions, project = "SRP009615", cutoff = 5L)
## You can then combine them into a single GRanges object if you want to
library("GenomicRanges")
single <- unlist(GRangesList(regs))
## End(Not run)
|
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