Define Sliding Window Regions

Source: R/define_regions.R

Generates overlapping fixed-size genomic windows for variant-set analysis.

define_regions_window(chr, start, end, window_size = 2000L, step_size = NULL)

Arguments

chr

Chromosome (integer or character).

start

Integer start position. Required.

end

Integer end position. Required.

window_size

Integer window width in bp. Default 2000.

step_size

Integer step between windows. Default window_size/2 (50% overlap).

Value

Data frame with columns: region_id, chr, start, end, label.

Examples

# 2kb windows with 50% overlap (default)
wins <- define_regions_window(chr = 22, start = 16570000, end = 16580000)
wins
#>   region_id chr    start      end                   label
#> 1     win_1  22 16570000 16571999 chr22:16570000-16571999
#> 2     win_2  22 16571000 16572999 chr22:16571000-16572999
#> 3     win_3  22 16572000 16573999 chr22:16572000-16573999
#> 4     win_4  22 16573000 16574999 chr22:16573000-16574999
#> 5     win_5  22 16574000 16575999 chr22:16574000-16575999
#> 6     win_6  22 16575000 16576999 chr22:16575000-16576999
#> 7     win_7  22 16576000 16577999 chr22:16576000-16577999
#> 8     win_8  22 16577000 16578999 chr22:16577000-16578999
#> 9     win_9  22 16578000 16579999 chr22:16578000-16579999

# 5kb non-overlapping windows
wins2 <- define_regions_window(chr = 1, start = 1000000, end = 1050000,
                               window_size = 5000, step_size = 5000)