removeSpots {arrayMagic}R Documentation

Remove specified spots from objects

Description

All elements matching the strings in spotsToBeRemoved are taken out of the object arrayDataObject and the corresponding ones out of the object exprSetRGObject as well, if supplied.

Usage

removeSpots(arrayDataObject, exprSetRGObject=NULL, spotsToBeRemoved=NULL, spotIdentifier="Name")

Arguments

arrayDataObject object of type arrayData; required; default: missing
exprSetRGObject object of type exprSetRG; optional; default: NULL
spotIdentifier character string, i.e. name of the column of getSpotAttr(arrayDataObject) used for matching; default "Name"
spotsToBeRemoved vector of character strings; default: NULL

Details

Value

A named list containing an object of type arrayData labelled "arrayDataObject", an object of type exprSetRG labelled "exprSetRGObject" and an integer specifying the number of removed items labelled "nrOfRemovedItems".

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

arrayData-class, exprSetRG-class

Examples


  intensities <- array(data=runif(600),dim=c(100,2,3))
  dimnames(intensities) <- list(NULL, c("green","red"), NULL)
  arrayDataObject <- new("arrayData", intensities=intensities, spotAttr=data.frame(Name=I(rep(c("x","y","Blank","Blank","z"),20))), hybAttrList=NULL)
  res <- removeSpots(arrayDataObject, spotsToBeRemoved=c("x","z"))
  stopifnot( dim(getIntensities(res[["arrayDataObject"]]))[1] == 3*20 )

   
  

[Package arrayMagic version 1.8.0 Index]