get_binom_ligation_threshold: Get self ligation threshold

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

This function calculates a self ligation threshold according to a method based on that of Heidari et al. (2014).

Usage

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

Arguments

GIObject	A GenomicInteractions object of paired end reads.
max.distance	Integer scalar specifying the maximum distance to consider between reads. Reads further apart than this distance should be very unlikely to be self ligations.
bin.size	Integer sclaar containing the bin size in base pairs.
p.cutoff	Numeric scalar specifying the p-value cut off for a significant difference from 50:50.
adjust	String specifying the method to use to adjust p-values, passed to p.adjust. This can also be NA for no adjustment.
plot	Logical scalar specifying whether to plot the percentage of reads on opposite strands vs difference, as well as the binomial test p value vs distance.

Details

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.

Value

Integer scalar specifying the cutoff in base pairs, below which an interaction is likely to be a self ligation.

References

Heidari N et al. (2014). Genome-wide map of regulatory interactions in the human genome. Genome Res. 24(12), 1905-1917.

LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.