asExprSet: converts a Ringo MAList into an ExpressionSet

In Ringo: R Investigation of ChIP-chip Oligoarrays

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

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

  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. 8, 2020, 5:34 p.m.