simulateMultivariate: Simulate multivariate data

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

Simulate known states, read counts and read coordinates using a multivariate Hidden Markov Model.

Usage

simulateMultivariate(
  bins,
  transition,
  emissions,
  weights,
  correlationMatrices,
  combstates,
  IDs,
  fragLen = 50
)

Arguments

bins	A GRanges-class object for which reads will be simulated.
transition	A matrix with transition probabilities.
emissions	A list() with data.frames with emission distributions (see uniHMM entry 'distributions').
weights	A list() with weights for the three univariate states.
correlationMatrices	A list with correlation matrices.
combstates	A vector with combinatorial states.
IDs	A character vector with IDs.
fragLen	Length of the simulated read fragments.

Value

A list() with entries $bins containing the simulated states and read count, $reads with simulated read coordinates.

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.