processAlignments: Read probe alignments from a directory

In VladaMilch/pdProbeRemap: What the package does (short line)

Description

Reads probe alignment files and creates an Alignments object

Usage

processAlignments(alignment.dir = NA)

Arguments

alignment.dir

the path to a directory that contains genomic and transcriptomic alignments

Details

This funtion reads genomic alignment file (Aligned.out.sam postfix required) and transcriptomic alignment file (Aligned.toTranscriptome.out.bam postfix requires) and generated an object of class "Alignments"

Value

a "Alignments".

Author(s)

Vladislava Milchevskaya [e-mail]

Examples

sam_file <- 
   dir(system.file("extdata",package="pdProbeRemap"), 
   pattern="example_drosophila.Aligned.out.sam",full.names=TRUE)
alignment_dir <- 
   strsplit(sam_file,  split = "example_drosophila.Aligned.out.sam")[[1]]
Als <- processAlignments(alignment_dir)

VladaMilch/pdProbeRemap documentation built on May 28, 2019, 3:21 p.m.