simulateUnivariate: Simulate univariate data

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

Description

Simulate known states, read counts and read coordinates using a univariate Hidden Markov Model with three states ("zero-inflation", "unmodified" and "modified").

Usage

simulateUnivariate(bins, transition, emission, fragLen = 50)

Arguments

bins	A GRanges-class object for which reads will be simulated.
transition	A matrix with transition probabilities.
emission	A data.frame with emission distributions (see uniHMM entry 'distributions').
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 and $transition and $emission.

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