bed_makewindows: Divide intervals into new sub-intervals ("windows").

In jayhesselberth/valr: Genome Interval Arithmetic

Divide intervals into new sub-intervals ("windows").

Description

Divide intervals into new sub-intervals ("windows").

Usage

bed_makewindows(x, win_size = 0, step_size = 0, num_win = 0, reverse = FALSE)

Arguments

x	ivl_df
win_size	divide intervals into fixed-size windows
step_size	size to step before next window
num_win	divide intervals to fixed number of windows
reverse	reverse window numbers

Value

ivl_df with .win_id column that contains a numeric identifier for the window.

Note

The name and .win_id columns can be used to create new interval names (see 'namenum' example below) or in subsequent group_by operations (see vignette).

See Also

Other utilities: bed12_to_exons(), bound_intervals(), flip_strands(), interval_spacing()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~name, ~score, ~strand,
  "chr1", 100,    200,  "A",   ".",    "+"
)

bed_glyph(bed_makewindows(x, num_win = 10), label = ".win_id")

# Fixed number of windows
bed_makewindows(x, num_win = 10)

# Fixed window size
bed_makewindows(x, win_size = 10)

# Fixed window size with overlaps
bed_makewindows(x, win_size = 10, step_size = 5)

# reverse win_id
bed_makewindows(x, win_size = 10, reverse = TRUE)

# bedtools 'namenum'
wins <- bed_makewindows(x, win_size = 10)
dplyr::mutate(wins, namenum = stringr::str_c(name, "_", .win_id))

jayhesselberth/valr documentation built on April 8, 2024, 12:32 p.m.