doACNE: (ACNE)

In HenrikBengtsson/ACNE: Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

(ACNE)

Description

(ACNE) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems.

Usage

  ## S3 method for class 'AffymetrixCelSet'
doACNE(csR, fln=FALSE, drop=TRUE, verbose=FALSE, ...)
  ## Default S3 method:
doACNE(dataSet, ..., verbose=FALSE)

Arguments

csR, dataSet	An AffymetrixCelSet (or the name of an AffymetrixCelSet).
fln	If TRUE, CRMAv2-style PCR fragment-length normalization is performed, otherwise not.
drop	If TRUE, the RMA summaries are returned, otherwise a named list of all intermediate and final results.
verbose	See Verbose.
...	Additional arguments used to set up AffymetrixCelSet (when argument dataSet is specified).

Value

Returns a named list, iff drop == FALSE, otherwise a named list of AromaUnitTotalCnBinarySet and AromaUnitFracBCnBinarySet.

Author(s)

Henrik Bengtsson

References

[1] M. Ortiz-Estevez, H. Bengtsson, A. Rubio, ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays, Bioinformatics, 2010 [PMC2913655].

HenrikBengtsson/ACNE documentation built on Feb. 20, 2024, 8:20 p.m.