RmmquantClass-class: An S4 class for Rmmquant.

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

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.

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