makeGenomicInteractionsFromFile: Create GenomicInteraction objects from a file
In LTLA/fugi: Further Utilities for Genomic Interactions

Description Usage Arguments Details Value Author(s) References Examples

Create GenomicInteractions objects from a variety of file formats. The resulting objects contain information on which genomic regions are interacting with each other, and the number of counts (usually for read pairs) supporting each interaction.

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makeGenomicInteractionsFromFile(fn, type = c("chiapet.tool", "bed12",
  "bedpe", "hiclib", "homer", "bam", "two.bams"), experiment_name = "",
  description = "", chr_names = NULL)

`fn`	String containing a path to the file (or for `type="hiclib"`, directory) containing the interaction data.
`type`	String specifying the format of `fn`.
`experiment_name`	String containing the experiment name.
`description`	String describing the experiment.
`chr_names`	Character vector of chromosome names in order, required for re-naming chromosomes with `type="hiclib"`.

This function reads interaction data from a variety of file formats including:

BAM files (single or double)
BED variants such as BED12 and BEDPE
Output of standard processing pipelines such as HOMER and ChIA-PET tool

For type="hiclib", the function expects that fn contains a path to the directory in which the files were extracted using h5dictToTxt.py from the hdf5 file. Note that recent versions of hiclib (2015-) cannot export the required data and so this function will only work with older files.

A GenomicInteractions object containing information extracted from fn.

Malcolm Perry, Elizabeth Ing-Simmons

Heinz S, Benner C, Spann N, Bertolino E et al. (2010). Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38(4), 576-589.

Li G et al. (2010). ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 11, R22,

k562.rep1 <- makeGenomicInteractionsFromFile(
    system.file(package="fugi", "extdata", "k562.rep1.cluster.pet3+.txt"),
    type="chiapet.tool", experiment_name="k562", description="k562 pol2 8wg16")

k562.rep1