RmmquantRun: Main Rmmquant function.

In Rmmquant: RNA-Seq multi-mapping Reads Quantification Tool

Description

Main Rmmquant function.

Usage

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)

Arguments

annotationFile	The annotation file
readsFiles	The reads files
genomicRanges	The annotation, in a GenomicRanges format.
genomicRangesList	The annotation, in a GenomicRangesList format.
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.

Value

A SummerizedExperiment.

Examples

dir <- system.file("extdata", package="Rmmquant", mustWork = TRUE)
gtfFile <- file.path(dir, "test.gtf")
samFile <- file.path(dir, "test.sam")
table <- RmmquantRun(gtfFile, samFile)

Rmmquant documentation built on Jan. 7, 2021, 2 a.m.