Merge an edgeR edgeR::DGEList() object using a clustering of the sites.
Arguments
- yall
A
edgeR::DGEList()object, where yall$genes is a metadata data frame with the locus coordinates (see details), and these fields at minimum: "Chr", "EntrezID", "Symbol", and "Strand".- new_clusters
A character vector. Contains the clustering solution of the sites in
yall.
Value
A new edgeR::DGEList() object that represents the clusters
Details
The yall object has a metadata framework yall$genes. This data frame has either a "Locus" field or
a pair of fields ("LocStart", "LocEnd"). Assuming that there are no clusters that merge sites across different
chromosomes and that clusters represent a continuous window in the genome, the function goes over the
clustering solutions in new_clusters and merges the sites from the same cluster.
The new genomic features contain the sum of counts of their sites, and the merged metadata of the sites
(e.g., a comma separated character with all gene symbols associated with the cluster).
See example of the full RRBS read count data pre-processing pipeline in analyze_tile().