cdfenvs {altcdfenvs}R Documentation

functions related to cdfenvs

Description

A set of functions to handle cdfenvs

Usage

wrapCdfEnvAffy(cdfenv, nrow.chip, ncol.chip, chiptype)
getCdfEnvAffy(abatch)
buildCdfEnv.matchprobes(matches, ids, probes.pack, abatch=NULL,
                        nrow.chip=NULL, ncol.chip=NULL, chiptype=NULL,
                        mm=NA, simplify = TRUE,
                        x.colname = "x", y.colname = "y")

Arguments

abatch an AffyBatch
cdfenv A cdfenv environment
chiptype A name for the chip type
ids a vector of probe set identifiers for the matches
matches a list as returned by the function matchprobes
mm The value to store for MMs
ncol.chip The number of columns for the chip type
nrow.chip The number of rows for the chip type
probes.pack The name of the probe package
simplify Simplify the environment created by removing the ids without any matching probe
x.colname, y.colname see the getxy.probeseq

Details

The class CdfEnv is defined as S3 to ensure compatibility with what is existing while changes are made. Migration to S4 is likely to happen after that...

Value

An instance of class CdfEnv.

Examples

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