segmenter

segmenter performs chromatin segmentation analysis in R by calling ChromHMM to integrate histone modification ChIP-seq datasets and learn chromatin states de-novo.

Key Features:

• ChromHMM Integration: Calls ChromHMM from within R to perform chromatin segmentation analysis.
• S4 Object Output: Captures ChromHMM output files in an S4 object for downstream processing.
• Bioconductor Interfacing: Interfaces with other relevant Bioconductor analysis tools.
• Output Testing: Provides functions to test the output of the segmentation.
• Model Selection: Provides functions to select among segmentation outputs.
• Visualization: Provides functions to visualize the output of the segmentation.

Scientific Applications:

• Chromatin State Annotation: Predicts underlying chromatin states from observed histone modification signals using a multivariate Markov model.
• Epigenomic Analysis: Integrates multiple histone modification ChIP-seq datasets for de-novo learning of chromatin states across the genome.

Methodology:

Transforms ChIP-seq data into signals over the genome, which represent observed states in a multivariate Markov model to predict chromatin's underlying states.