gr.setdiff: 'BiocGenerics::setdiff' shortcut (strand agnostic)

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

BiocGenerics::setdiff shortcut (strand agnostic)

Description

Shortcut for BiocGenerics::setdiff

gr1 <- GRanges(1, IRanges(10,20), strand="+") gr2 <- GRanges(1, IRanges(15,25), strand="-") gr3 <- "1:1-15" gr1 gr1

More robust and faster implementation of GenomicRanges::setdiff()

Robust to common edge cases of setdiff(gr1, gr2) where gr2 ranges are contained inside gr1's (yieldings setdiffs yield two output ranges for some of the input gr1 intervals.

Usage

x %_% ...

gr.setdiff(query, subject, ignore.strand = TRUE, by = NULL, ...)

Arguments

x	GRanges object to to
...	arguments to be passed to gr.findoverlaps
query	GRanges object as query
subject	GRanges object as subject
ignore.strand	boolean Flag to ignore strands. Refer to 'gr.findoverlaps()'. (default = TRUE)
by	vector Meta-data column to consider when performing overlaps. Refer to 'gr.findoverlaps()' documentation (default = NULL)

Value

GRanges representing setdiff of input interval

Returns indices of query in subject. If none found, NA

Author(s)

Marcin Imielinski

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