get_self_ligation_threshold {GenomicInteractions} | R Documentation

## Get self ligation threshold with SD method from Heidari et al

### Description

This function calculates a self ligation threshold according to the method published in Heidari et al., Genome Research, 2014. Briefly, paired reads are divided into in evenly sized bins. For each bin, the log2 ratio of reads that are aligned to opposite strand vs 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-liagted reads.

### Usage

    get_self_ligation_threshold(
      GIObject,
      bins = 100,
      distance_th = 400000,
      plot = TRUE
    )

### Arguments

`GIObject` | a GInteractions object of paired end reads
`bins` | Number of evenly sized bins to use.
`distance_th` | The threshold, in base pairs, to use as a cutoff to pick which bins to use to determine the standard deviation.
`plot` | TRUE by default. Whether to plot the log2ratio of opposite to same strand reads vs distance.

### Value

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

[Package GenomicInteractions version 1.24.0 Index]