get_self_ligation_threshold

a GInteractions object of paired end reads

GIObject

bins

The threshold, in base pairs, to use as a cutoff to 
pick which bins to use to determine the standard deviation.

distance_th

TRUE by default. Whether to plot the log2ratio of opposite
to same strand reads vs distance.

plot


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.


R package for handling Genomic interaction data, such as
ChIA-PET/Hi-C, annotating genomic features with interaction
information and producing various plots / statistics.

Malcolm Perry

GenomicInteractions

R package for handling genomic interaction data

get_self_ligation_threshold function

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.

get_self_ligation_threshold: Get self ligation threshold with SD method from Heidari et al

Description

Usage

Arguments

Value