loadBAM: Load BAM files

In chernolab/ASpli: Analysis of Alternative Splicing Using RNA-Seq

Description

Load BAM files into R session using a targets specification.

Usage

 loadBAM(targets, cores,  libType, strandMode) 

Arguments

targets	A data frame containing sample, bam and experimental factors columns
cores	Number of processors to use
libType	Options are: "SE" or "PE"
strandMode	Options are: 0,1,2. See ?strandMode for more information

Value

A list of GAlignments or GAlignmentPairs . Each element of the list correspond to a samples BAM file.

Author(s)

Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

Examples

  # Define bam files, sample names and experimental factors for targets.
  #bamFileNames <- c( "A_C_0.bam", "A_C_1.bam", "A_C_2.bam", 
  #                   "A_D_0.bam", "A_D_1.bam", "A_D_2.bam" )
  
  #targets <- data.frame( 
  #             row.names = paste0('Sample_',c(1:6)),
  #             bam = system.file( 'extdata', bamFileNames, package="ASpli" ),
  #             factor1 = c( 'C','C','C','D','D','D') )
               
  # Load reads from bam files
  #bams <- loadBAM( targets )
  

chernolab/ASpli documentation built on March 11, 2021, 12:24 a.m.