buildCdfEnv.biostrings {altcdfenvs}R Documentation

Build CDF environments

Description

Build CDF environment from Biostrings matchPDict results

Usage

buildCdfEnv.biostrings(apm, abatch = NULL,
                       nrow.chip = NULL, ncol.chip = NULL,
                       simplify = TRUE,
                       x.colname = "x", y.colname = "y",
                       verbose = FALSE)

Arguments

apm AffyProbesMatch
abatch AffyBatch
nrow.chip number of rows for the chip type (see details)
ncol.chip number of columns for the chip type (see details)
simplify simplify the environment built (removing target names when there is no matching probe)
x.colname column name
y.colname column name
verbose verbose TRUE/FALSE

Details

Whenever an abatch is specified, nrow.chip and ncol.chip are not needed. Specifying the an AffyBatch in abatch is the easiest way to specify information about the geometry of a chip type.

Value

An instance of class CdfEnvAffy.


[Package altcdfenvs version 2.4.0 Index]