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Genomic distance bias correction.

Source: R/OverExpectedHiC.R
OverExpectedHiC.Rd

Function that normalises HiC matrices by expected values computed per genomic distance.

Usage

OverExpectedHiC(
  hicLst,
  method = "mean_non_zero",
  verbose = FALSE,
  cores = 1,
  plot_contact_vs_dist = "per_seq"
)

Arguments

hicLst

<ListContactMatrix>: The HiC maps list.

method

Options are "mean_non_zero", "mean_total", or "lieberman". Look at details for more. (Default: "mean_non_zero")

verbose

: Show the progression in console? (Default FALSE)

cores

: Number of cores to be used. (Default 1)

plot_contact_vs_dist

Whether to plot contact vs distance curve per chromosome ("per_seq"), all chromosomes ("total") or not (NULL). (Default "per_seq")

Value

A matrices list.

Details

OverExpectedHiC

Methods to calculate expected values per distance:

  • "mean_non_zero": for each distance, average contact value is calculated using only non-zero values.

  • "mean_total": for each distance, average contact value is calculated using all values at this distance.

  • "lieberman": for each distance, contact values are summed and divided by chromsome length minus distance. Only for cis contacts.

Examples

# Note: run HicAggR::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] 1e+05
#> 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.
#> # ℹ 243 more rows