RmmquantRun {Rmmquant} | R Documentation

## Main Rmmquant function.

### 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)

[Package Rmmquant version 1.12.0 Index]