asExprSet: converts a Ringo MAList into an ExpressionSet

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/preprocess.R

Description

Function to convert an object of class MAList into an object of class ExpressionSet. Note that the otherwise optional targets component is required in this case to generate the phenoData of the new ExpressionSet.

Usage

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asExprSet(from, idColumn="PROBE_ID")

Arguments

from

object of class MAList to convert into an ExpressionSet

idColumn

string; indicating which column of the genes data.frame of the MAList holds the identifier for reporters on the microarray. This column, after calling make.names on it, will make up the unique featureNames of the resulting ExpressionSet.

Value

an object of class ExpressionSet

Note

There is a more general function for converting MALists to ExpressionSets in the package convert. This function here is solely intended for converting Ringo-generated MALists into ExpressionSets.

Author(s)

Joern Toedling

See Also

ExpressionSet, preprocess

Examples

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  exDir <- system.file("exData",package="Ringo")
  exRG  <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
  exMA  <- preprocess(exRG, "none", returnMAList=TRUE)
  exX   <- asExprSet(exMA)

Ringo documentation built on Nov. 17, 2017, 9:44 a.m.