justmmgMOS: Compute mmgmos Directly from CEL Files

Description Usage Arguments Details Value See Also

View source: R/justmmgmos.R

Description

This function converts CEL files into an exprReslt using mmgmos.

Usage

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justmmgMOS(..., filenames=character(0),
          widget=getOption("BioC")$affy$use.widgets,
          compress=getOption("BioC")$affy$compress.cel,
          celfile.path=getwd(),
          sampleNames=NULL,
          phenoData=NULL,
          description=NULL,
          notes="",
          background=TRUE, gsnorm=c("median", "none", "mean", "meanlog"), savepar=FALSE, eps=1.0e-6)

just.mmgmos(..., filenames=character(0),
           phenoData=new("AnnotatedDataFrame"),
           description=NULL,
           notes="",
           compress=getOption("BioC")$affy$compress.cel,
           background=TRUE, gsnorm=c("median", "none", "mean", "meanlog"), savepar=FALSE, eps=1.0e-6)

Arguments

...

file names separated by comma.

filenames

file names in a character vector.

widget

a logical specifying if widgets should be used.

compress

are the CEL files compressed?

celfile.path

a character denoting the path where cel files locate.

sampleNames

a character vector of sample names to be used in the FeatureSet.

phenoData

an AnnotatedDataFrame object.

description

a MIAME object

notes

notes

background

Logical value. If TRUE, then perform background correction before applying mmgmos.

gsnorm

character. specifying the algorithm of global scaling normalisation.

savepar

Logical value. If TRUE, the the estimated parameters of the model are saved in file par\_mmgmos.txt and phi\_mmgmos.txt.

eps

Optimisation termination criteria.

Details

This method should require much less RAM than the conventional method of first creating an FeatureSet and then running mmgmos.

Note that this expression measure is given to you in log base 2 scale. This differs from most of the other expression measure methods.

The algorithms of global scaling normalisation can be one of "median", "none", "mean", "meanlog". "mean" and "meanlog" are mean-centered normalisation on raw scale and log scale respectively, and "median" is median-centered normalisation. "none" will result in no global scaling normalisation being applied.

Value

An exprReslt.

See Also

Related class exprReslt-class and related method mmgmos


puma documentation built on Nov. 8, 2020, 11:08 p.m.