boundingIndices: Find indices of features bounding a set of chromosome ranges/genes

Description

This function is similar to findOverlaps but it guarantees at least two features will be covered. This is useful in the case of finding features corresponding to a set of genes. Some genes will fall entirely between two features and thus would not return any ranges with findOverlaps. 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

boundingIndices(starts, stops, positions, all.indices = FALSE)

Arguments

starts

integer vector of first base position of each query range

stops

integer vector of last base position of each query range

positions

Base positions in which to search

all.indices

logical, return a list containing full sequence of indices for each query

Value

integer matrix of 2 columms for start and stop index of range in data or a list of full sequences of indices for each query (see all.indices argument)

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. boundingIndices does not check for NAs or unsorted data in the subject positions. These assumptions are safe for position info coming from a GenoSet or GRanges.

Examples

Run this code

starts = seq(10,100,10)
  boundingIndices( starts=starts, stops=starts+5, positions = 1:100 )