Perform MA normalization on a hic.table object

MA_norm(
  hic.table,
  degree = 2,
  Plot = FALSE,
  span = NA,
  loess.criterion = "gcv"
)

Arguments

hic.table	A hic.table object
degree	The degree for loess normalization
Plot	logical, should the MA plot be output?
span	The span for loess. If left as the default value of NA the span will be calculated automatically
loess.criterion	The criterion for calculating the span for loess

Value

An extended hic.table with adjusted IFs and M columns.

Details

Performs loess normalization on the MA plot of the data.

Examples

# create hic.table
data("HMEC.chr22")
data("NHEK.chr22")
hic.table <- create.hic.table(HMEC.chr22, NHEK.chr22, chr= 'chr22')
# Plug hic.table into MA_norm()
MA_norm(hic.table)
#>        chr1   start1     end1  chr2   start2     end2  IF1         IF2 D
#>    1: chr22 16000000 16500000 chr22 16000000 16500000    5    5.203323 0
#>    2: chr22 16000000 16500000 chr22 16500000 17000000    2    8.672206 1
#>    3: chr22 16500000 17000000 chr22 16500000 17000000  297  480.440193 0
#>    4: chr22 16000000 16500000 chr22 17000000 17500000    5   14.742750 2
#>    5: chr22 16500000 17000000 chr22 17000000 17500000   92  277.510581 1
#>   ---                                                                   
#> 2479: chr22 49000000 49500000 chr22 51000000 51500000   21   54.634896 4
#> 2480: chr22 49500000 50000000 chr22 51000000 51500000   35   71.112086 3
#> 2481: chr22 50000000 50500000 chr22 51000000 51500000  394  339.083241 2
#> 2482: chr22 50500000 51000000 chr22 51000000 51500000 4066 2741.284207 1
#> 2483: chr22 51000000 51500000 chr22 51000000 51500000 9916 7132.021930 0
#>                 M      adj.IF1     adj.IF2      adj.M           mc         A
#>    1:  0.05750528     6.536565    3.980167 -0.7157038  0.773209076  2.350681
#>    2:  2.11639897     2.569759    6.749430  1.3931324  0.723266529  2.058199
#>    3:  0.69389392   296.785580  480.787300  0.6959778 -0.002083871  8.561266
#>    4:  1.56000562     6.682254   11.031270  0.7231921  0.836813540  3.101931
#>    5:  1.59283701    92.872125  274.904590  1.5656134  0.027223570  7.319980
#>   ---                                                                       
#> 2479:  1.37943338    25.579092   44.854321  0.8102819  0.569151461  5.082034
#> 2480:  1.02273986    40.614557   61.281551  0.5934559  0.429283962  5.640653
#> 2481: -0.21655615   393.572489  339.451564 -0.2134236 -0.003132504  8.513774
#> 2482: -0.56875831  4168.551419 2673.845292 -0.6406301  0.071871832 11.705015
#> 2483: -0.47544713 10117.157776 6990.217117 -0.5333949  0.057947745 13.037819