normalize: Normalization and cellularity adjustment for arrayCGH data.

In tgac-vumc/CGHcall: Calling aberrations for array CGH tumor profiles.

Description

This function normalizes arrayCGH data using the global mode or median. It can also adjust for the cellularity of your data.

Usage

normalize(input, method = "median", smoothOutliers = TRUE, ...)

Arguments

input	Object of class cghRaw.
method	Normalization method, either median, mode, or none.
smoothOutliers	Logical. Indicates whether outliers should be smoothed using the smooth.CNA function.
...	Arguments for smooth.CNA.

Details

The cellularity parameter should be a vector of length n where n is the number of samples in your dataset. The vector is recycled if there are not enough values in it, or truncated if there are too many. For more information on the correction we refer to section 1.6 of the supplementary information for van de Wiel et al. 2006.

Value

This function returns a dataframe in the same format as the input with normalized and/or cellularity adjusted log2 ratios.

Author(s)

Sjoerd Vosse & Mark van de Wiel

Examples

  data(Wilting)
  ## Convert to 'cghRaw' object
  cgh <- make_cghRaw(Wilting)
  ## First preprocess the data
  raw.data <- preprocess(cgh)
  ## Simple global median normalization for samples with 75% tumor cells
  normalized.data <- normalize(raw.data)

tgac-vumc/CGHcall documentation built on May 31, 2019, 9 a.m.