countReads: count mapped reads overlap genomic intervals

In TCseq: Time course sequencing data analysis

Description

This function counts mapped reads from multiple BAM files that overlap genomic intervals in genomicFeature in a TCA object. The counting result is stored in 'count' slot of the TCA object.

Usage

countReads(object, dir, method = "summarizeoverlaps", zero.based = TRUE,
  ...)

Arguments

object	a TCA object
dir	character string giving the directory where BAM files are stored.
method	character string giving the counting method. Options are 'summarizeOverlaps' and 'featureCounts'. For Windows system, only 'summarizeOverlaps' can be used, For Linux system, both methods can be used.
zero.based	Logical. If TRUE, the start positions of the genomic intervals are 0-based, if FALSE, the start positions will be 1-based.
...	additional arguments passed to summarizeOverlaps and featureCounts in Rsubread package

Details

This function provides two options 'summarizeOverlaps' from GenomicAlignments package and featureCounts' from Rsubread package to count the aligned reads. As Rsubread package is only avaible for linux systems, Windows users can only use 'summarizeOverlaps'. The user could specify counting details by passing additional arguments (...), otherwise the default settings of the two methods are used. For counting details, see summarizeOverlaps, featureCounts in Rsubread package

Value

A TCA object with updated 'count' slot.

Author(s)

Mengjun Wu

See Also

summarizeOverlaps, featureCounts in Rsubread package

TCseq documentation built on Nov. 8, 2020, 5:46 p.m.