run.model.fitting: run.model.fitting

In chicane: Capture Hi-C Analysis Engine

Description

Run model fitting procedure for either bait-to-bait or other interactions. Meant for internal use only.

Usage

run.model.fitting(
  interaction.data,
  distance.bins = NULL,
  distribution = "negative-binomial",
  bait.to.bait = FALSE,
  adjustment.terms = NULL,
  maxit = 100,
  epsilon = 1e-08,
  cores = 1,
  trace = FALSE,
  verbose = FALSE,
  interim.data.dir = NULL
)

Arguments

interaction.data	data.table object containing interaction counts. Must contain columns distance, count, and bait_trans_count.
distance.bins	Number of bins to split distance into. Models are fit separately in each bin.
distribution	Name of distribution of the counts. Options are 'negative-binomial', 'poisson', 'truncated-poisson', and 'truncated-negative-binomial'
bait.to.bait	Logical indicating if model should be fit as bait-to-bait
adjustment.terms	Characted vector of extra terms to adjust for in the model fit
maxit	Maximum number of IWLS iterations for fitting the model (passed to glm.control)
epsilon	Positive convergence tolerance for Poisson and negative binomial models. Passed to glm.control
cores	Integer value specifying how many cores to use to fit model for cis-interactions.
trace	Logical indicating if output should be produced for each of model fitting procedure. Passed to glm.control or gamlss.control
verbose	Logical indicating whether to print progress reports.
interim.data.dir	Path to directory to store intermediate QC data and plots.

Value

Interactions data with expeceted number of interactions and p-values added.

chicane documentation built on Nov. 7, 2021, 1:07 a.m.