11  Functional enrichment analysis of genomic coordinations

Functional analysis using NGS data (e.g., RNA-Seq and ChIP-Seq) can be performed by linking coding and non-coding regions to coding genes via the r Biocpkg("ChIPseeker") (Yu, Wang, and He 2015) package, which can annotate genomic regions to their nearest genes, host genes, and flanking genes respectively. In addition, it provides a function, seq2gene, that simultaneously considers host genes, promoter regions and flanking genes from intergenic regions that may be under control via cis-regulation. This function maps genomic regions to genes in a many-to-many manner and facilitates functional analysis. For more details, please refer to r Biocpkg("ChIPseeker") (Yu, Wang, and He 2015).

References

Yu, Guangchuang, Li-Gen Wang, and Qing-Yu He. 2015. “ChIPseeker: An r/Bioconductor Package for ChIP Peak Annotation, Comparison and Visualization.” Bioinformatics 31 (14): 2382–83. https://doi.org/10.1093/bioinformatics/btv145.