join_overlap_intersect {plyranges}R Documentation

Join by overlapping Ranges

Description

Join by overlapping Ranges

Usage

join_overlap_intersect(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))

join_overlap_intersect_within(x, y, maxgap, minoverlap, suffix = c(".x",
  ".y"))

join_overlap_intersect_directed(x, y, maxgap, minoverlap,
  suffix = c(".x", ".y"))

join_overlap_intersect_within_directed(x, y, maxgap, minoverlap,
  suffix = c(".x", ".y"))

join_overlap_inner(x, y, maxgap = -1L, minoverlap = 0L,
  suffix = c(".x", ".y"))

join_overlap_inner_within(x, y, maxgap = -1L, minoverlap = 0L,
  suffix = c(".x", ".y"))

join_overlap_inner_directed(x, y, maxgap = -1L, minoverlap = 0L,
  suffix = c(".x", ".y"))

join_overlap_inner_within_directed(x, y, maxgap = -1L, minoverlap = 0L,
  suffix = c(".x", ".y"))

join_overlap_left(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))

join_overlap_left_within(x, y, maxgap, minoverlap, suffix = c(".x",
  ".y"))

join_overlap_left_directed(x, y, maxgap, minoverlap, suffix = c(".x",
  ".y"))

join_overlap_left_within_directed(x, y, maxgap, minoverlap,
  suffix = c(".x", ".y"))

Arguments

x, y

Objects representing ranges

maxgap, minoverlap

The maximimum gap between intervals as an integer greater than or equal to zero. The minimum amount of overlap between intervals as an integer greater than zero, accounting for the maximum gap.

suffix

Character to vectors to append to common columns in x and y (default = c(".x", ".y")).

Details

The function join_intersect_overlaps finds the genomic intervals that are the overlapping ranges between x and y and returns a new ranges object with metadata columns from x and y.

The function join_inner_overlaps is equivalent to find_overlaps.

The function join_left_overlaps performs a left outer join between x and y. It returns all ranges in x that overlap or do not overlap ranges in y plus metadata columns common to both. If there is no overlapping range the metadata column will contain a missing value.

The function join_self_overlaps find all overlaps between a ranges object x and itself.

All of these functions have two suffixes that modify their behavior. The within suffix, returns only ranges in x that are completely contained in y. The directed suffix takes into account the strandedness of a GRanges object.

Value

a GRanges object

Examples

x <- as_iranges(data.frame(start = c(11, 101), end = c(21, 201)))
y <- as_iranges(data.frame(start = c(10, 20, 50, 100),
                           end = c(19, 21, 105, 202)))

# intersect takes common interval
join_overlap_intersect(x,y)

# within
join_overlap_intersect_within(x,y)


[Package plyranges version 1.4.4 Index]