metagene (version 1.0.0)

parseBamFiles: Parse multiple bamFiles

Description

This function will fetch the aligned reads from multiple bam files that overlap with a list of regions.

Usage

parseBamFiles( bamFiles, featuresGroups, cores=1)

Arguments

bamFiles

A vector of bam files

featuresGroups

A list of data.frame. One data.frame by group of features. The names of each element of the list correspond to the name of the group.

cores

Number of cores for parallel processing (require parallel package).

Value

parseBamFiles returns a list of list of list that contains the raw counts for every features groups.

Examples

  # Get a bam file name
  ## Not run: bamFileName <- system.file("extdata/align1_rep1.bam", package="metagene")

  # Load a feature file
  ## Not run: featuresFileName <- system.file("extdata/list1.txt", package="metagene")
  ## Not run: features <- metagene:::prepareFeatures(featuresFileName, specie="mouse")

  # Parse multiple bam files
  ## Not run: bam <- metagene:::parseBamFiles(bamFileName, features)