cdfenv: functions related to cdfenvs

In altcdfenvs: alternative CDF environments (aka probeset mappings)

Description

A set of functions to handle cdfenvs

Usage

wrapCdfEnvAffy(cdfenv, nrow.chip, ncol.chip, chiptype, check = TRUE,
               verbose = FALSE)
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", verbose=FALSE)

Arguments

abatch	an AffyBatch
cdfenv	A cdfenv environment
check	perform consistency check or not
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 combineAffyBatch
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
verbose	verbosity (TRUE or FALSE)

Value

An instance of class CdfEnvAffy.

Examples

## See the main vignette

altcdfenvs documentation built on Nov. 8, 2020, 7:12 p.m.