RmmquantClass-class {Rmmquant} | R Documentation

## An S4 class for Rmmquant.

### Description

An S4 class for Rmmquant.

### Slots

`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.

`counts`

  A `SummarizedExperiment` storing the counts.

[Package Rmmquant version 1.12.0 Index]