ICE: Quick and dirty implementation of ICE matrix normalization

In qenvio/dryhic: Some Functions to Handle HiC Data

Description

This function takes a contact matrix (tipically the output of get_contacts_matrix and performs ICE normalization

Usage

ICE(mat, itermax = 1, maxdev = 0.1, verbose = TRUE)

Arguments

mat	A contact matrix (could be the output of get_contacts_matrix)
maxdev	Maximum relative deviation from the mean of the correction factor
verbose	Logical indicating if progression messages should be turned on
intermax	Maximum number of iterations

Value

A named sparse_matrix containing the normalized number of contacts per pair of genomic bins at the requested region plus the b attribute containing the vector of correction factors

References

@articleimakaev2012iterative, title=Iterative correction of Hi-C data reveals hallmarks of chromosome organization, author=Imakaev, Maxim and Fudenberg, Geoffrey and McCord, Rachel Patton and Naumova, Natalia and Goloborodko, Anton and Lajoie, Bryan R and Dekker, Job and Mirny, Leonid A, journal=Nature methods, volume=9, number=10, pages=999–1003, year=2012, publisher=Nature Publishing Group

Examples

plot(0)

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