MA_norm: Perform MA normalization on a hic.table object

Description Usage Arguments Details Value Examples

View source: R/MA_norm.R

Description

Perform MA normalization on a hic.table object

Usage

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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

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# 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/HiCdiff documentation built on May 20, 2019, 11:13 a.m.