Package 'Rmmquant'

Title: RNA-Seq multi-mapping Reads Quantification Tool
Description: RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.
Authors: Zytnicki Matthias [aut, cre]
Maintainer: Zytnicki Matthias <[email protected]>
License: GPL-3
Version: 1.23.0
Built: 2024-09-28 04:45:07 UTC
Source: https://github.com/bioc/Rmmquant

Help Index

Get the counts table of an RmmquantClass object.

Description

Get the counts table of an RmmquantClass object.

Usage

counts(object)

## S4 method for signature 'RmmquantClass'
counts(object)

Arguments

object

An RmmquantClass object.

Value

The count matrix, in a SummarizedExperiment

Examples

example <- RmmquantClassExample()
counts(example)

Rmmquant: RNA-Seq multi-mapping Reads Quantification Tool

Description

Counts the number of reads per gene.

Author(s)

Matthias Zytnicki, [email protected]

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.

Example of Rmmquant constructor.

Description

Example of Rmmquant constructor.

Usage

RmmquantClassExample()

Value

An RmmquantClass.

Examples

example <- RmmquantExample()

Example of Rmmquant use

Description

Example of Rmmquant use

Usage

RmmquantExample()

Value

An SummarizedExperiement.

Examples

example <- RmmquantExample()

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)

Show the content of an RmmquantClass object.

Description

Show the content of an RmmquantClass object.

Usage

## S4 method for signature 'RmmquantClass'
show(object)

Arguments

object

An RmmquantClass object.

Value

A description of the object.

Examples

example <- RmmquantClassExample()
example

Rmmquant object validation function.

Description

Rmmquant object validation function.

Usage

validateRmmquant(object)

Arguments

object

A RmmquantClass object.

Value

TRUE, if succeed, otherwise a character.