Analysis of ChIP-seq Data with ‘mosaics’ Package

This vignette provides an introduction to the analysis of ChIP-seq data with ‘mosaics’ package. R package mosaics implements MOSAiCS, a statistical framework for the analysis of ChIP-seq data, proposed in [1]. MOSAiCS stands for“MOdel-based one and two Sample Analysis and Inference for ChIP-Seq Data”. Based on careful investigation of biases in ChIP-seq data such as mappability and GC content, MOSAiCS has been developed as a flexible mixture modeling approach for detecting peaks of one-sample (ChIP sample) or two-sample (ChIP sample and matched control sample) ChIP-seq data. ‘mosaics’ package assumes chromosome-wise analysis of ChIP-seq data. In this vignette, we use chromosome 22 of the data from a ChIP-seq experiment of STAT1 binding in interferon-γstimulated HeLa S3 cells from [2] The package can be loaded with the command: