Function that normalises HiC matrices by expected values computing by genomic distance.
Arguments
- hic.cmx_lst
<List[contactMatrix]>: The HiC maps list.
- verbose.bln
<logical>: If TRUE show the progression in console. (Default FALSE)
- cores.num
<numerical> : Number of cores to be used. (Default 1)
Examples
# Note: run Genomic2DTK::BalanceHiC before OverExpectedHiC calculation.
data(HiC_Ctrl.cmx_lst)
OverExpectedHiC(HiC_Ctrl.cmx_lst)
#> $`2L_2L`
#> class: ContactMatrix
#> dim: 236 236
#> type: dgCMatrix
#> rownames: NULL
#> colnames: NULL
#> metadata(6): name type ... resolution expected
#> regions: 236
#>
#> $`2L_2R`
#> class: ContactMatrix
#> dim: 236 253
#> type: dgCMatrix
#> rownames: NULL
#> colnames: NULL
#> metadata(6): name type ... resolution expected
#> regions: 489
#>
#> $`2R_2R`
#> class: ContactMatrix
#> dim: 253 253
#> type: dgCMatrix
#> rownames: NULL
#> colnames: NULL
#> metadata(6): name type ... resolution expected
#> regions: 253
#>
#> attr(,"resolution")
#> [1] 100000
#> attr(,"chromSize")
#> # A tibble: 2 × 3
#> name length dimension
#> <chr> <dbl> <dbl>
#> 1 2L 23513712 236
#> 2 2R 25286936 253
#> attr(,"matricesKind")
#> # A tibble: 3 × 4
#> name type kind symmetric
#> <chr> <chr> <chr> <lgl>
#> 1 2L_2L cis U TRUE
#> 2 2L_2R trans NA FALSE
#> 3 2R_2R cis U TRUE
#> attr(,"mtx")
#> [1] "o/e"
#> attr(,"expected")
#> # A tibble: 253 × 2
#> distance expected
#> <dbl> <dbl>
#> 1 1 44559.
#> 2 100001 12794.
#> 3 200001 3665.
#> 4 300001 2130.
#> 5 400001 1445.
#> 6 500001 1092.
#> 7 600001 876.
#> 8 700001 739.
#> 9 800001 625.
#> 10 900001 550.
#> # … with 243 more rows