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

Usage

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

Arguments

x

ivl_df

genome

this argument has been deprecated and is not used

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

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)
#> # A tibble: 10 × 7
#>    chrom start   end name  score strand .win_id
#>    <chr> <int> <int> <chr> <chr> <chr>    <int>
#>  1 chr1    100   110 A     .     +            1
#>  2 chr1    110   120 A     .     +            2
#>  3 chr1    120   130 A     .     +            3
#>  4 chr1    130   140 A     .     +            4
#>  5 chr1    140   150 A     .     +            5
#>  6 chr1    150   160 A     .     +            6
#>  7 chr1    160   170 A     .     +            7
#>  8 chr1    170   180 A     .     +            8
#>  9 chr1    180   190 A     .     +            9
#> 10 chr1    190   200 A     .     +           10

# Fixed window size
bed_makewindows(x, win_size = 10)
#> # A tibble: 10 × 7
#>    chrom start   end name  score strand .win_id
#>    <chr> <int> <int> <chr> <chr> <chr>    <int>
#>  1 chr1    100   110 A     .     +            1
#>  2 chr1    110   120 A     .     +            2
#>  3 chr1    120   130 A     .     +            3
#>  4 chr1    130   140 A     .     +            4
#>  5 chr1    140   150 A     .     +            5
#>  6 chr1    150   160 A     .     +            6
#>  7 chr1    160   170 A     .     +            7
#>  8 chr1    170   180 A     .     +            8
#>  9 chr1    180   190 A     .     +            9
#> 10 chr1    190   200 A     .     +           10

# Fixed window size with overlaps
bed_makewindows(x, win_size = 10, step_size = 5)
#> # A tibble: 20 × 7
#>    chrom start   end name  score strand .win_id
#>    <chr> <int> <int> <chr> <chr> <chr>    <int>
#>  1 chr1    100   110 A     .     +            1
#>  2 chr1    105   115 A     .     +            2
#>  3 chr1    110   120 A     .     +            3
#>  4 chr1    115   125 A     .     +            4
#>  5 chr1    120   130 A     .     +            5
#>  6 chr1    125   135 A     .     +            6
#>  7 chr1    130   140 A     .     +            7
#>  8 chr1    135   145 A     .     +            8
#>  9 chr1    140   150 A     .     +            9
#> 10 chr1    145   155 A     .     +           10
#> 11 chr1    150   160 A     .     +           11
#> 12 chr1    155   165 A     .     +           12
#> 13 chr1    160   170 A     .     +           13
#> 14 chr1    165   175 A     .     +           14
#> 15 chr1    170   180 A     .     +           15
#> 16 chr1    175   185 A     .     +           16
#> 17 chr1    180   190 A     .     +           17
#> 18 chr1    185   195 A     .     +           18
#> 19 chr1    190   200 A     .     +           19
#> 20 chr1    195   200 A     .     +           20

# reverse win_id
bed_makewindows(x, win_size = 10, reverse = TRUE)
#> # A tibble: 10 × 7
#>    chrom start   end name  score strand .win_id
#>    <chr> <int> <int> <chr> <chr> <chr>    <int>
#>  1 chr1    100   110 A     .     +           10
#>  2 chr1    110   120 A     .     +            9
#>  3 chr1    120   130 A     .     +            8
#>  4 chr1    130   140 A     .     +            7
#>  5 chr1    140   150 A     .     +            6
#>  6 chr1    150   160 A     .     +            5
#>  7 chr1    160   170 A     .     +            4
#>  8 chr1    170   180 A     .     +            3
#>  9 chr1    180   190 A     .     +            2
#> 10 chr1    190   200 A     .     +            1

# bedtools 'namenum'
wins <- bed_makewindows(x, win_size = 10)
dplyr::mutate(wins, namenum = stringr::str_c(name, '_', .win_id))
#> # A tibble: 10 × 8
#>    chrom start   end name  score strand .win_id namenum
#>    <chr> <int> <int> <chr> <chr> <chr>    <int> <chr>  
#>  1 chr1    100   110 A     .     +            1 A_1    
#>  2 chr1    110   120 A     .     +            2 A_2    
#>  3 chr1    120   130 A     .     +            3 A_3    
#>  4 chr1    130   140 A     .     +            4 A_4    
#>  5 chr1    140   150 A     .     +            5 A_5    
#>  6 chr1    150   160 A     .     +            6 A_6    
#>  7 chr1    160   170 A     .     +            7 A_7    
#>  8 chr1    170   180 A     .     +            8 A_8    
#>  9 chr1    180   190 A     .     +            9 A_9    
#> 10 chr1    190   200 A     .     +           10 A_10