simulateMultivariate: Simulate multivariate data

Description Usage Arguments Value

View source: R/simulate.R

Description

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

Usage

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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 May 2, 2020, 2:01 a.m.