prepare.data {chicane}

prepare.data

Description

Prepare data for running interaction calling. Takes a BAM file and baits and restriction fragments as input, and returns a data table with data ready for analysis.

Usage

prepare.data(
  bam,
  baits,
  fragments,
  replicate.merging.method = "sum",
  include.zeros = c("none", "cis", "all"),
  remove.adjacent = FALSE,
  temp.directory = NULL,
  keep.files = FALSE,
  verbose = FALSE
)

Arguments

bam

Path to a BAM file

baits

Path to a BED file containing the baits

fragments

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

replicate.merging.method

Method that should be used for merging replicates, if applicable

include.zeros

String specifying what zero counts to include. Options are none (default), cis, and all.

remove.adjacent

Logical indicating whether to remove all reads mapping to adjacent restriction fragments.

temp.directory

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

keep.files

Logical indicating whether to keep temporary files

verbose

Logical indicating whether to print progress reports.

Value

Data table object with columns

target.id

String in chrN:start-end format identifying target fragment

bait.id

String in chrN:start-end format identifying bait fragment

target.chr

Chromosome of target fragment

target.start

Start coordinate of target fragment (zero-based)

target.end

End coordinate of target fragment

bait.chr

Chromosome of bait fragment

bait.start

Start coordinate of bait fragment (zero-based)

bait.end

End coordinate of bait fragment

bait.to.bait

Boolean indicating if the interaction is bait-to-bait (i.e. the fragment listed as target is also a bait)

count

The number of reads linking the two fragments

bait.trans.count

The number of reads linking the bait to fragments in trans (a measure of "interactibility")

target.trans.count

The number of reads linking the target to fragments in trans (a measure of "interactibility")

distance

Distance between the midpoints of the bait and target fragments (basepairs). NA for trans interactions

Examples

if( bedtools.installed() ) {
  bam <- system.file('extdata', 'Bre80_2q35.bam', package = 'chicane');
  baits <- system.file('extdata', '2q35.bed', package = 'chicane');
  fragments <- system.file('extdata', 'GRCh38_HindIII_chr2.bed.gz', package = 'chicane');
  input.data <- prepare.data(
	bam = bam, 
	baits = baits, 
	fragments = fragments
	);
 }