readXml: (Advanced) Read XML files of Affymetrix sample attriubtes or...

In AffyCompatible: Affymetrix GeneChip software compatibility

Description

This functions reads the content of Affymetrix DTT (MAGE) or ARR sample files, or AffxNetAffxAnnotFile array annotation files, return an internal representation of the underlying XML. The return value can be used with xclass to rapidly create R objects representing deeply nested nodes of the document. The return value can also be used with xpathApply in the XML package for access to character-based representation of the data.

Usage

readXml(fl, ...)

Arguments

fl	A length-1 character vector giving the full path to the file to be parsed.
...	Additional arguments, passed to xmlTreeParse.

Value

An object of class XMLInternalDocument.

Author(s)

Martin Morgan

See Also

The vignettes ‘Retrieving MAGE and ARR sample attributes’ and ‘Annotation retrieval with NetAffxResource’ for detailed illustration of use.

xclass for instantiating objects from xpath queries.

Examples

mageDir <- system.file("extdata", "DTT", package="AffyCompatible")
mageFiles <- list.files(mageDir, full=TRUE)
xml <- readXml(mageFiles[[1]])
xclass(xml, "//MeasuredBioAssay")[[1]]

AffyCompatible documentation built on Nov. 8, 2020, 8:15 p.m.