grl.in: Check intersection of 'GRangesList' with windows on genome

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

Check intersection of GRangesList with windows on genome

Description

Check intersection of GRangesList with windows on genome

Like only if the ranges in grl[i] intersect <<all>>, <<some>>, <<only>> windows in the subject

e.g. can use to identify read pairs whose ends are contained inside two genes)

Usage

grl.in(
  grl,
  windows,
  some = FALSE,
  only = FALSE,
  logical = TRUE,
  exact = FALSE,
  ignore.strand = TRUE,
  ...
)

Arguments

grl	GRangesList object to query for membership in windows
windows	GRanges pile of windows
some	boolean Will return TRUE for GRangesList elements that intersect at least on window range (default = FALSE)
only	boolean Will return TRUE for GRangesList elements only if there are no elements of query that fail to intersect with windows (default = FALSE)
logical	boolean Will return logical otherwise will return numeric vector of number of windows overlapping each grl (default = TRUE)
exact	boolean Will return exact intersection (default = FALSE)
ignore.strand	boolean Will return exact intersection (default = TRUE)
...	Additional parameters to be passed on to GenomicRanges::findOverlaps
maxgap	integer maxgap is interpreted as the max gap allowed between two ranges to be considered as overlapping. See documentation for IRanges::findOverlaps() (default = -1L)

Value

boolean vector of match status

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