Divides the values of track expression into segments by using Wilcoxon test.
gsegment(
expr = NULL,
minsegment = NULL,
maxpval = 0.05,
onetailed = TRUE,
intervals = NULL,
iterator = NULL,
intervals.set.out = NULL
)track expression
minimal segment size
maximal P-value that separates two adjacent segments
if 'TRUE', Wilcoxon test is performed one tailed, otherwise two tailed
genomic scope for which the function is applied
track expression iterator of "fixed bin" type. If 'NULL' iterator is determined implicitly based on track expression.
intervals set name where the function result is optionally outputted
If 'intervals.set.out' is 'NULL' a set of intervals where each interval represents a segment.
This function divides the values of track expression into segments, where each segment size is at least of 'minsegment' size and the P-value of comparing the segment with the first 'minsegment' values from the next segment is at most 'maxpval'. Comparison is done using Wilcoxon (also known as Mann-Whitney) test.
If 'intervals.set.out' is not 'NULL' the result is saved as an intervals set. Use this parameter if the result size exceeds the limits of the physical memory.
# \dontshow{
options(gmax.processes = 2)
# }
gdb.init_examples()
gsegment("dense_track", 5000, 0.0001)
#> chrom start end
#> 1 chr1 0 9200
#> 2 chr1 9200 31550
#> 3 chr1 31550 41350
#> 4 chr1 41350 65600
#> 5 chr1 65600 75800
#> 6 chr1 75800 99150
#> 7 chr1 99150 121800
#> 8 chr1 121800 129250
#> 9 chr1 129250 150650
#> 10 chr1 150650 157850
#> 11 chr1 157850 162900
#> 12 chr1 162900 224200
#> 13 chr1 224200 246200
#> 14 chr1 246200 309950
#> 15 chr1 309950 326350
#> 16 chr1 326350 346700
#> 17 chr1 346700 352200
#> 18 chr1 352200 362000
#> 19 chr1 362000 369400
#> 20 chr1 369400 379300
#> 21 chr1 379300 384800
#> 22 chr1 384800 426600
#> 23 chr1 426600 433950
#> 24 chr1 433950 500000
#> 25 chr2 0 28400
#> 26 chr2 28400 33600
#> 27 chr2 33600 38950
#> 28 chr2 38950 45800
#> 29 chr2 45800 50800
#> 30 chr2 50800 75600
#> 31 chr2 75600 85150
#> 32 chr2 85150 90600
#> 33 chr2 90600 99600
#> 34 chr2 99600 116150
#> 35 chr2 116150 122550
#> 36 chr2 122550 143400
#> 37 chr2 143400 154050
#> 38 chr2 154050 184350
#> 39 chr2 184350 194450
#> 40 chr2 194450 199600
#> 41 chr2 199600 207250
#> 42 chr2 207250 224400
#> 43 chr2 224400 229400
#> 44 chr2 229400 246000
#> 45 chr2 246000 276550
#> 46 chr2 276550 300000
#> 47 chrX 0 11300
#> 48 chrX 11300 16350
#> 49 chrX 16350 90000
#> 50 chrX 90000 95000
#> 51 chrX 95000 106200
#> 52 chrX 106200 116800
#> 53 chrX 116800 127850
#> 54 chrX 127850 135050
#> 55 chrX 135050 153450
#> 56 chrX 153450 200000