join_overlap_intersect {plyranges} | R Documentation |
Join by overlapping Ranges
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"))
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 = |
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.
a GRanges object
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)