RmmquantRun {Rmmquant} | R Documentation |
Main Rmmquant function.
RmmquantRun(annotationFile = "", readsFiles = character(0), genomicRanges = GRanges(), genomicRangesList = GRangesList(), sampleNames = character(0), overlap = NA_integer_, strands = character(0), sorts = logical(0), countThreshold = NA_integer_, mergeThreshold = NA_real_, printGeneName = FALSE, quiet = TRUE, progress = FALSE, nThreads = 1, formats = character(0), nOverlapDiff = NA_integer_, pcOverlapDiff = NA_real_, lazyload = FALSE)
annotationFile |
The annotation file |
readsFiles |
The reads files |
genomicRanges |
The annotation, in a
|
genomicRangesList |
The annotation, in a
|
sampleNames |
The name of the samples |
overlap |
The minimum number of overlapping base pairs to declare a match. |
strands |
Whether annotation of the same strand should be considered. |
sorts |
Whether the files are sorted. |
countThreshold |
The reads files |
mergeThreshold |
The reads files |
printGeneName |
Whether the (vernacular) gene name is reported. |
quiet |
Shut Rmmquant up. |
progress |
Print the progress of the tool. |
nThreads |
The number of threads. |
formats |
The format of the reads files (SAM or BAM). |
nOverlapDiff |
Difference of overlap between a primary map and a secondary map. |
pcOverlapDiff |
Ratio of overlap between a primary map and a secondary map. |
lazyload |
Usual for S4 functions. |
A SummerizedExperiment
.
dir <- system.file("extdata", package="Rmmquant", mustWork = TRUE) gtfFile <- file.path(dir, "test.gtf") samFile <- file.path(dir, "test.sam") table <- RmmquantRun(gtfFile, samFile)