knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )
ChromHMM (Ernst & Kellis, 2012), an implementation of a hidden Markov model (HMM), uses epigenetic features such as histone modifications to represent observed (or output) states and unobserved (or hidden) states to represent chromatin states. Due to the nature of hidden states, the number of states will need to be specified programmatically and oftentimes numerous candidate models are generated. The goal of hmmpickr is to quantitatively help pick the model whose states are the most well-defined.
# install.packages("devtools") devtools::install_github("csiu/hmmpickr")
library(hmmpickr) # List of ChromHMM models model_files <- c( system.file("extdata", "model_roadmap15.txt", package="hmmpickr"), system.file("extdata", "model_roadmap18.txt", package="hmmpickr")) # Calculate homogeneity cost hmmpick(model_files, full_path = FALSE)
The list output of hmmpick()
is sorted by ascending homogeneity cost.
Therefore, the model in the first position is the model whose states are the
most well-defined.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.