convert.bam

Path to a BED file containing the baits

baits

Path to a BED file containing all restriction fragments in the genome

fragments

Directory where temporary files should be stored. Defaults to current directory.

temp.directory

Logical indicating whether to keep temporary files

keep.files

Convert a BAM file to a format that can be used for replicate merging.
Note: This function does not process data enough to be used for interaction calling. Use <code>prepare.data</code> for full preprocessing.

Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.

convert.bam: convert.bam

Description

Usage

Arguments

See Also