get_binom_ligation_threshold: get self ligation threshold with binomial test

In ComputationalRegulatoryGenomicsICL/GenomicInteractions: Utilities for handling genomic interaction data

get self ligation threshold with binomial test

Description

This function calculates a self ligation threshold according to a method based on that of Heidari et al., Genome Research, 2014. Briefly, paired reads are divided into in evenly spaced bins. For each bin, the number of reads that are aligned to opposite strand vs to the same strand is calculated. A binomial test is used to test if this is significantly different from the 50:50 ratio expected by chance if all reads are real interactions.

Usage

get_binom_ligation_threshold(
  GIObject,
  max.distance = 20000,
  bin.size = 500,
  p.cutoff = 0.05,
  adjust = "fdr",
  plot = TRUE
)

Arguments

GIObject	a GInteractions object of paired end reads
max.distance	The maximum distance to consider between reads. Reads further apart than this distance should be very unlikely to be self ligations.
bin.size	Bin size in base pairs.
p.cutoff	P value cut off for a significant difference from 50:50. Default: 0.05
adjust	Method to use to adjust p values. Default: fdr. See 'help(p.adjust)' for accepted values. Can also be NA for no adjustment.
plot	TRUE by default. Whether to plot the percentage of reads on opposite strands vs difference and the binomial test p value vs distance.

Value

The cutoff in base pairs below which an interaction is likely to be a self ligation.

ComputationalRegulatoryGenomicsICL/GenomicInteractions documentation built on April 16, 2022, 4:09 a.m.