preprocess: Preprocess arrayCGH data

Description Usage Arguments Details Value Author(s) References Examples

Description

This function preprocesses your aCGH data so it can be processed by other functions without errors.

Usage

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preprocess(input, maxmiss = 30, nchrom = 23, ...)

Arguments

input

Object of class cghRaw.

maxmiss

Maximum percentage of missing values per row.

nchrom

Number of chromosomes.

...

Arguments for impute.knn from the impute package.

Details

This function performs the following actions on arrayCGH data:

Value

This function returns a dataframe in the same format as the input with missing values imputed.

Author(s)

Sjoerd Vosse & Mark van de Wiel

References

Olga Troyanskaya, Michael Cantor, Gavin Sherlock, Pat Brown, Trevor Hastie, Robert Tibshirani, David Botstein, and Russ B. Altman (2001). Missing value estimation methods for DNA microarrays. Bioinformatics, 17, 520-525.

Examples

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  data(WiltingRaw)
  preprocessed <- preprocess(WiltingRaw, nchrom = 22)

CGHcall documentation built on Nov. 8, 2020, 11:12 p.m.