sample_hic_data: Sample data containing Hi-C contact maps as well as...

In rz6/DIADEM: Hi-C differential analysis via dependency modelling of chromatin interactions with generalized linear models

Description

The list contains 5 elements:

"IMR90-MboI-1"

List of raw Hi-C contact maps in sparse format (i.e.: data frame with columns: i,j,val,diagonal,name) from GSE63525 study. The list only contains contact map of chromosome 21, first replicate.

"MSC-HindIII-1"

List of raw Hi-C contact maps in sparse format (i.e.: data frame with columns: i,j,val,diagonal,name) from GSE52457 study. The list only contains contact map of chromosome 21, first replicate.

"HiCcomparator"

HiCcomparator object constructed from the above 2 datasets with parameters as indicated in vignette.

"HiCglm"

HiCglm object constructed from the above 2 datasets with parameters as indicated in vignette.

"chromosome.sizes"

List with names matching names (chromosomes) from first two datasets and values equal to their sizes (number of bins in contact map).

Usage

data(sample_hic_data)

Format

An object of class list of length 5.

rz6/DIADEM documentation built on Dec. 31, 2019, 3:51 a.m.