HiCDCPlus {HiCDCPlus} | R Documentation

## HiCDCPlus

### Description

This function finds significant interactions in a HiC-DC readable matrix and expresses statistical significance of counts through the following: 'pvalue': significance P-value, 'qvalue': FDR corrected P-value, mu': expected counts, 'sdev': modeled standard deviation of expected counts.

### Usage

    HiCDCPlus(
      gi_list,
      covariates = NULL,
      chrs = NULL,
      distance_type = "spline",
      model_distribution = "nb",
      binned = TRUE,
      df = 6,
      Dmin = 0,
      Dmax = 2e+06,
      ssize = 0.01,
      splineknotting = "uniform",
      model_filepath = NULL
    )

### Arguments

`gi_list` | List of `GenomicInteractions` objects where each object named with chromosomes contains intrachromosomal interaction information (minimally containing counts and genomic distance in `mcols(gi_list[[1]])`—see `?gi_list_validate` for a detailed explanation of valid `gi_list` instances).
`covariates` | covariates to be considered in addition to genomic distance D. Defaults to all covariates besides 'D','counts','mu','sdev',pvalue','qvalue' in `mcols(gi_list[[1]])`
`chrs` | select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes in the `gi_list`.
`distance_type` | distance covariate form: 'spline' or 'log'. Defaults to 'spline'.
`model_distribution` | 'nb' uses a Negative Binomial model, 'nb_vardisp' uses a Negative Binomial model with a distance specific dispersion parameter inferred from the data, 'nb_hurdle' uses the legacy HiCDC model.
`binned` | TRUE if uniformly binned or FALSE if binned by restriction enzyme fragment cutsites
`df` | degrees of freedom for the genomic distance spline function if `distance_type='spline'`. Defaults to 6, which corresponds to a cubic spline as explained in Carty et al. (2017)
`Dmin` | minimum distance (included) to check for significant interactions, defaults to 0
`Dmax` | maximum distance (included) to check for significant interactions, defaults to 2e6 or maximum in the data; whichever is minimum.
`ssize` | Distance stratified sampling size. Can decrease for large chromosomes. Increase recommended if model fails to converge. Defaults to 0.01.
`splineknotting` | Spline knotting strategy. Either "uniform", uniformly spaced in distance, or placed based on distance distribution of counts "count-based" (i.e., more closely spaced where counts are more dense).
`model_filepath` | Outputs fitted HiC-DC model object as an .rds file per chromosome. Defaults to NULL (no output).

### Value

A valid `gi_list` instance with additional `mcols(.)` for each chromosome: pvalue': significance P-value, 'qvalue': FDR corrected P-value, mu': expected counts, 'sdev': modeled standard deviation of expected counts.

### Examples

    gi_list<-generate_binned_gi_list(50e3,chrs='chr22')
    gi_list<-add_hic_counts(gi_list,
    hic_path<-system.file("extdata", "GSE63525_HMEC_combined_example.hic",
    package = "HiCDCPlus"))
    gi_list<-HiCDCPlus(gi_list)

[Package HiCDCPlus version 1.0.0 Index]