get_self_ligation_threshold: Get self ligation threshold
In LTLA/fugi: Further Utilities for Genomic Interactions

Description Usage Arguments Details Value References

Calculates a self ligation threshold according to the method published in Heidari et al. (2014).

1 2	get_self_ligation_threshold(GIObject, bins = 100, distance_th = 4e+05, plot = TRUE)

`GIObject`	A GenomicInteractions object of paired end reads.
`bins`	Integer scalar specifying the number of evenly sized bins to use.
`distance_th`	Integer scalar specifying the threshold on the distance (between anchors `GIObject`, in base pairs), to use as a cutoff to pick which bins to use to determine the standard deviation.
`plot`	Logical scalar specifying whether to plot the log2-ratio of opposite to same strand read pair frequences against the distance between anchoring reads.

Briefly, paired reads are divided into in evenly sized bins. For each bin, the log2-ratio of reads that are aligned to opposite strand versus to the same strand is calculated. Twice the standard deviation of this ratio at high distances is used a cutoff to determine which bins are likely to contain mostly self-ligated reads.

An integer scalar containing the cutoff in base pairs below which an interaction is likely to be a self ligation.

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.