MA_norm: Perform MA normalization on a hic.table object

In dozmorovlab/HiCcompare: HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Perform MA normalization on a hic.table object

Description

Perform MA normalization on a hic.table object

Usage

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

Details

Performs loess normalization on the MA plot of the data.

Value

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

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)

dozmorovlab/HiCcompare documentation built on June 30, 2023, 3:09 a.m.