gr.match: Alternative 'GenomicRanges::match' that accepts additional...

In mskilab/gUtils: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

Alternative GenomicRanges::match that accepts additional gr.findoverlaps options

Description

Alternative GenomicRanges::match that accepts additional gr.findoverlaps options

Wrapper to GenomicRanges::match (uses gr.findoverlaps). This allows users to match on additional by fields, or chunk into smaller pieces for lower memory.

Usage

gr.match(query, subject, max.slice = Inf, verbose = FALSE, ...)

Arguments

query	Query GRanges pile
subject	Subject GRanges pile
max.slice	max slice of query to match at a time
verbose	whether to give verbose outputx
...	Additional arguments to be passed along to gr.findoverlaps.

Value

Vector of length = length(query) with subject indices of *first* subject in query, or NA if none found. This behavior is different from gr.findoverlaps, which will return *all* indicies of subject in query (in the case of one query overlaps with multiple subject) ... = additional args for findOverlaps (IRanges version)

Author(s)

Marcin Imielinski

mskilab/gUtils documentation built on June 6, 2023, 12:08 a.m.