get_compartment.character: Calculate compartment scores

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

Calculate compartment scores

Description

Load Hi-C matrix from .hic file and calculate compartment scores.

Usage

## S3 method for class 'character'
get_compartment(
  hic_matrix,
  method = c("juicer", "lieberman", "obs_exp", "nonzero", "average", "fanc"),
  chrom = NULL,
  resol,
  reference = NULL,
  oe = c("juicer", "ht", "as-is"),
  genome = NULL,
  norm = c("NONE", "VC", "VC_SQRT", "KR", "SCALE"),
  ...
)

Arguments

resol	A positive integer for resolution.
genome	Name of the reference genome.

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