Preprocess BED-files with reads to calculate chromosome coverage

Description

Given a directory with BED-files describing ChIP-seq reads, makes coverage files (1 pr chromosome) describing tag counts along the chromosomes. Reads in all available BED-files in the given directory is first converted to IRanges objects and saved as RData files. The preprocessing ends by creating one file for each chromosome, with the calculated coverage on the different strands for different BED-files.

Usage

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preprocess(configPath = "./config.yml", params=list())

Arguments

configPath

Path to a configuration file in YAML format (see config.yml), or NULL.

params

A list of parameters (see details).

Details

The preprocess function computes the chromosome tag-coverage along each chromosome.
Parameters supplied in params can include the following:

  • READ.PATH Path to BED files with reads.

  • COVER.PATH Path for coverage files (preprocessing output).

  • READ.WIDTH Read width (w)

Value

Used for its side-effect.

Author(s)

Karl Kornacker <kornacker@midohio.twcbc.com> and Tony Handstad <tony.handstad@gmail.com>

Examples

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## Not run: 
# Run preprocessing using a configuration file in YAML format:
preprocces(configPath = "./config.yml")

# Run preprocessing without using a configuration file:
preprocces(configPath = NULL, params=list(READ.PATH="./tmp",
           COVER.PATH="./chrcovers", READ.WIDTH=100))

## End(Not run)