calcPartitions {GenomicDistributions} | R Documentation |
Takes a GRanges object, then assigns each element to a partition from the provided partitionList, and then tallies the number of regions assigned to each partition. A typical example of partitions is promoter, exon, intron, etc; this function will yield the number of each for a query GRanges object There will be a priority order to these, to account for regions that may overlap multiple genomic partitions.
calcPartitions( query, partitionList, remainder = "intergenic", bpProportion = FALSE )
query |
GRanges or GRangesList with regions to classify |
partitionList |
an ORDERED (if bpProportion=FALSE) and NAMED list of genomic partitions GRanges. This list must be in priority order; the input will be assigned to the first partition it overlaps. bpProportion=TRUE, the list does not need ordering. |
remainder |
A character vector to assign any query regions that do not overlap with anything in the partitionList. Defaults to "intergenic" |
bpProportion |
logical indicating if overlaps should be calculated based on number of base pairs overlapping with each partition. bpProportion=FALSE does overlaps in priority order, bpProportion=TRUE counts number of overlapping base pairs between query and each partition. |
A data.frame assigning each element of a GRanges object to a partition from a previously provided partitionList.
partitionList = genomePartitionList(geneModels_hg19$genesGR, geneModels_hg19$exonsGR, geneModels_hg19$threeUTRGR, geneModels_hg19$fiveUTRGR) calcPartitions(vistaEnhancers, partitionList)