| easyRNASeq island methods {easyRNASeq} | R Documentation |
Process the coverage to locate regions with a minimum coverage (min.cov). If regions are separated by a gap shorter than a maximum length (max.gap), they are unified. Only islands longer than min.length are returned. These functions are now outdated and would need to be actualized.
## S4 method for signature 'RNAseq' findIslands(obj, max.gap = integer(1), min.cov = 1L, min.length = integer(1), plot = TRUE, ...)
obj |
An object of class |
max.gap |
Maximum gap between two peaks to build an island |
min.cov |
Minimum coverage for an island to be returned |
min.length |
Minimum size of an island to be returned |
plot |
If TRUE, draw plots of coverage distribution. Help the user to select an appropriate value for the minimum coverage. |
... |
See details |
... are for providing additional options to the
hist plot function.
An RNAseq object with the readIsland slot set with a
RangedData containing the selected islands and the readCount slot
actualized with a list containing the count table per island.
Nicolas Delhomme
## Not run:
# NOTE that this function might need to be actualized
obj <- new('RNAseq',
organismName="Dmelanogaster",
readLength=36L,
chrSize=as.list(seqlengths(Dmelanogaster))
)
library(curl)
invisible(sapply(c("ACACTG","ACTAGC"),function(bam){
curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/",
"master/tutorial/easyRNASeq/",bam,".bam"),paste0(bam,".bam"))
curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/",
"master/tutorial/easyRNASeq/",bam,".bam.bai"),paste0(bam,".bam.bai"))
}))
obj <- fetchCoverage(obj,format="bam",filename="ACACTG.bam")
obj <- findIslands(
obj,
max.gap=10L,
min.cov=10L,
min.length=200L)
## End(Not run)