genoset (version 1.28.2)

boundingIndicesByChr: Find indices of features bounding a set of chromosome ranges/genes, across chromosomes

Description

Finds subject ranges corresponding to a set of genes (query ranges), taking chromosome into account. Specifically, this function will find the indices of the features (first and last) bounding the ends of a range/gene (start and stop) such that first

Usage

boundingIndicesByChr(query, subject)

Arguments

query

GRanges or something coercible to GRanges

subject

GenomicRanges

Value

• integer matrix with two columns corresponding to indices on left and right bound of queries in subject

Details

This function uses some tricks from findIntervals, where is for k queries and n features it is O(k * log(n)) generally and ~O(k) for sorted queries. Therefore will be dramatically faster for sets of query genes that are sorted by start position within each chromosome. The index of the stop position for each gene is found using the left bound from the start of the gene reducing the search space for the stop position somewhat.

This function differs from boundingIndices in that 1. it uses both start and end positions for the subject, and 2. query and subject start and end positions are processed in blocks corresponding to chromosomes.

Both query and subject must be in at least weak genome order (sorted by start within chromosome blocks).

See Also

Other "range summaries": boundingIndices, rangeSampleMeans