get_compartment.ht_table: Calculate compartment scores

In haizi-zh/hictools: Home-made handy tools for Hi-C

Calculate compartment scores

Description

Calculate compartment scores for Hi-C matrix in ht_table format.

Usage

## S3 method for class 'ht_table'
get_compartment(
  hic_matrix,
  method = c("juicer", "lieberman", "obs_exp", "nonzero", "average", "fanc"),
  chrom = NULL,
  reference = NULL,
  oe = c("juicer", "ht", "as-is"),
  juicertools = get_juicer_tools(),
  java = "java",
  ...
)

Arguments

hic_matrix

A ht_table object for the Hi-C matrix.

haizi-zh/hictools documentation built on June 29, 2022, 4:32 a.m.