summariseByFeaturePairs {GenomicInteractions} | R Documentation |
This function will calculate the number of observed interactions between two sets of features provided by the end-user. This allows the summarisation of the number of features of a specific type a particular region is involved in and how many interactions exist between them.
summariseByFeaturePairs(GIObject, features.one, feature.name.one, features.two, feature.name.two) ## S4 method for signature 'GInteractions' summariseByFeaturePairs(GIObject, features.one, feature.name.one, features.two, feature.name.two)
GIObject |
An annotated GInteractions object |
features.one |
A GRanges object containing the feature set of interest |
feature.name.one |
The name of the first feature set of interest |
features.two |
A GRanges object containing the second feature set of interest |
feature.name.two |
The name of the second feature set of interest |
A data frame with one line for each range in ‘features’
data("hic_example_data") data("mm9_refseq_promoters") data("thymus_enhancers") annotateInteractions(hic_example_data, list(promoter = mm9_refseq_promoters, enhancer = thymus_enh)) # can be slow so subset of features used for examples p <- unique(unlist(head(regions(hic_example_data)$promoter.id))) e <- unique(unlist(head(regions(hic_example_data)$enhancer.id))) p <- p[!is.na(p)] p <- mm9_refseq_promoters[p] e <- e[!is.na(e)] e <- thymus_enh[e] ep_summary <- summariseByFeaturePairs(hic_example_data, p, "promoter", e, "enhancer")