overlap-joins: Join by overlapping Ranges

In sa-lee/plyranges: A fluent interface for manipulating GenomicRanges

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_overlap_intersect() 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_overlap_inner() is equivalent to find_overlaps().

The function join_overlap_left() 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_overlap_self() 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 overlapped within in y. The directed suffix accounts for the strandedness of the ranges when performing overlaps.

Value

a GRanges object

See Also

join_overlap_self(), join_overlap_left(), find_overlaps()

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, 1),
                           end = c(19, 21, 105, 202, 5)))

# self
join_overlap_self(y)

# intersect takes common interval
join_overlap_intersect(x,y)

# within
join_overlap_intersect_within(x,y)

# left, and inner join, it's often useful having an id column here
y <- y %>% mutate(id = 1:n()) 
x <- x %>% mutate(id = 1:n()) 
join_overlap_inner(x,y)
join_overlap_left(y,x, suffix = c(".left", ".right"))

sa-lee/plyranges documentation built on April 15, 2024, 12:25 p.m.