Description Usage Arguments Value References Examples
This function takes a contact matrix (tipically the output of get_contacts_matrix
and performs ICE normalization
1 |
mat |
A contact matrix (could be the output of |
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 |
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
@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
1 | plot(0)
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