rMAT

rMAT identifies enriched regions from ChIP-chip experiments using Affymetrix tiling arrays to locate transcription factor binding sites and chromatin or histone modifications at genomic scale.

Key Features:

• R package: Implements algorithms for analysis of ChIP-chip tiling array data within R.
• BPMAP and CEL handling: Parses and merges Affymetrix BPMAP and CEL tiling array files for downstream analysis.
• C++ Fusion SDK and affxparser integration: Integrates the C++ Fusion SDK and Bioconductor affxparser for low-level reading and preprocessing of Affymetrix tiling array files.
• Sequence-specific normalization: Applies sequence-specific models to normalize tiling array intensities.
• Raw intensity processing: Processes raw microarray intensities from Affymetrix tiling arrays.
• Fast algorithmic framework: Implements a fast algorithmic framework to efficiently identify enriched regions in ChIP-chip data.

Scientific Applications:

• Transcription factor binding mapping: Identification and genomic mapping of transcription factor binding sites from ChIP-chip data.
• Chromatin and histone modification detection: Detection of genomic regions enriched for chromatin or histone modifications.
• DNA–protein interaction analysis: Analysis of DNA–protein interactions at genomic scale using tiling array data.
• Genome-wide ChIP-chip studies: High-throughput, genome-wide analysis of ChIP-chip experiments generated on Affymetrix tiling arrays.

Methodology:

Parses and merges BPMAP and CEL files using the C++ Fusion SDK and Bioconductor affxparser, applies sequence-specific normalization models to raw microarray intensities, and uses an algorithmic framework implemented in R with C++ components to detect enriched regions.