Aligning tracks with HiCExperiment objects

# S4 method for class 'HiCExperiment'
coverage(x, use.pairs = FALSE, bin.size = resolution(x))

Arguments

x: A HiCExperiment object over a full genome
use.pairs: logical. Whether to use pairsFile to compute Hi-C coverage
bin.size: if use.pairs == TRUE, to which resolution

Value

A HiCExperiment object with 2 added columns in regions(x)

Examples

mcool_file <- HiContactsData::HiContactsData('yeast_wt', format = 'mcool')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
hic <- import(mcool_file, format = 'mcool', resolution = 1000)
coverage(hic)
#> RleList of length 16
#> $I
#> numeric-Rle of length 230000 with 221 runs
#>   Lengths:        1000        1000        1000 ...        1000        1000
#>   Values :     50.6400     41.8479     57.0913 ...   1.1989167   0.0570913
#> 
#> $II
#> numeric-Rle of length 813000 with 807 runs
#>   Lengths:      1000      1000      3000 ...      1000      1000      1000
#>   Values :   6.56550  10.33352   0.00000 ...   2.39783   0.00000   0.45673
#> 
#> $III
#> numeric-Rle of length 315000 with 312 runs
#>   Lengths:      1000      1000      1000 ...      1000      1000      1000
#>   Values :  27.11835  43.50355  75.24630 ...  107.0461   81.5834   57.3767
#> 
#> $IV
#> numeric-Rle of length 1526000 with 1503 runs
#>   Lengths:       1000       1000       1000 ...       1000       1000
#>   Values :   0.114183   0.856369   4.396028 ...    23.8642    10.3335
#> 
#> $V
#> numeric-Rle of length 572000 with 564 runs
#>   Lengths:      1000      1000      1000 ...      1000      1000      1000
#>   Values :  11.18989   6.33713   3.02584 ...   44.8737   20.7241    5.8804
#> 
#> ...
#> <11 more elements>