reproducibility_score: Compute the reproducibility score between two contact...

In qenvio/dryhic: Some Functions to Handle HiC Data

Description

This function takes a couple of contact matrices and computes the reproducibility score.

Usage

reproducibility_score(mat1, mat2, r = 20, mipr = 5, na.rm = TRUE)

Arguments

mat1	A dgTMatrix of contacts with genomic bins as row.names.
mat2	Another dgTMatrix of contacts with genomic bins as row.names.
r	The number of componentes used in the comparison.
mipr	Threshold for the j-inverse participation ratio (IPR).
na.rm	logical indicating if bins with NA should be removed.

Details

Please note that mat1 and mat2 are expected to be a matrices of one chromosome (you could obtain them using subset_matrix).

Value

The reproducibility score between two matrices.

References

https://doi.org/10.1093/bioinformatics/btx152

Examples

plot(0)

qenvio/dryhic documentation built on March 17, 2020, 8:37 p.m.