gr.merge: merge GRanges by using coordinates as primary key

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

merge GRanges by using coordinates as primary key

Description

Uses gr.findoverlaps() to enable internal and external joins of GRanges using syntax similar to "merge" where merging is done using coordinates +/- "by" fields

Uses gr.findoverlaps() / GRanges::findOverlaps for heavy lifting, but returns outputs with metadata populated as well as query and subject ids. For external joins, overlaps x with gaps(y) and gaps(x) with y.

Usage

gr.merge(
  query,
  subject,
  by = NULL,
  all = FALSE,
  all.query = all,
  all.subject = all,
  ignore.strand = TRUE,
  verbose = FALSE,
  ...
)

Arguments

query	GRanges Set of GRanges to query. Refer to gr.findoverlaps() and GenomicRanges::findOverlaps()
subject	GRanges Set of GRanges as 'subject' in query. Refer to gr.findoverlaps() and GenomicRanges::findOverlaps()
by	vector Additional metadata fields to join on
all	boolean Flag whether to include left and right joins
all.query	boolean Flag whether to do a left join (default = all)
all.subject	boolean Flag whether to do a right join (default = all)
ignore.strand	boolean Strand information ignored (default = TRUE)
verbose	boolean

Value

GRanges merged on 'by' vector

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