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 These functions are now outdated and would need to be actualized.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)