get_compartment: Calculate compartment scores using Juicer tools
In haizi-zh/hictools: Home-made handy tools for Hi-C

get_compartment

R Documentation

Calculate compartment scores using Juicer tools

Description

Calculate compartment scores using Juicer tools

Usage

get_compartment(
  hic_matrix,
  method = c("juicer", "lieberman", "obs_exp", "nonzero", "average", "fanc"),
  chrom = NULL,
  reference = NULL,
  oe = c("juicer", "ht", "as-is"),
  norm = c("NONE", "VC", "VC_SQRT", "KR", "SCALE"),
  ...
)

Arguments

`hic_matrix`	Either a `ht_table` object, or the path of the `.hic` name. If a file path, `resol` cannot be NULL since we can't infer resolution directly from the `.hic` file.
`chrom`	A character vector indicating which chromosomes to run. If `NULL`, will calculate compartment scores for all chromosomes. However, in this case, `hic_matrx` cannot be the `.hic` file name.
`reference`	A reference compartment track which is used to "orient" principal components. If `NULL`, no orienting will be performed. Can be the name of a pre-computed reference track, e.g. gc.GRCh38.500kbp (see `data(package = "hictools")`), or path to the bed file for the reference track, or a `GRanges` object.
`oe`	The method to compute observed/expected values. `"juicer"` indicates using using the values computed by Juicer tools. `"ht"` indicates using hictools for the calculation. `"as-is"` indicates observed values will be used as observed/expected ones, thus skipping the OE calculation. This may be useful when the input is cofrag matrix rather than standard Hi-C data. Won't take effect if `method` is `"juicer"`.
`norm`	The norm used for calculating compartment scores. If `hic_matrix` is not a `.hic` file name, `norm` will be ignored.
`resol`	Resolution of the matrix. Must be a positive integer when the input is a Hi-C file.