removeSpots {arrayMagic} | R Documentation |
all elements matching the strings in spotsToBeRemoved
are taken out of the object arrayDataObject
and if
supplied out of the object exprSetArrayObject
as well
arrayDataObject |
object of type arrayData ; required; default missing |
exprSetArrayObject |
object of type exprSetArray ; optional; default NULL |
spotIdentifier |
character strings name of the appropriate column; default "Name" |
spotsToBeRemoved |
vector of character strings; default NULL |
list containing
an object of type arrayData
labelled arrayDataObject
and an integer specifying the number of removed items
labelled nrOfRemovedItems
and possily an object of type exprSetArray
labelled exprSetArrayObject
Andreas Buness <a.buness@dkfz.de>
intensities <- array(data=runif(600),dim=c(100,2,3)) dimnames(intensities) <- list(NULL, c("Cy3","Cy5"), NULL) arrayDataObject <- new("arrayData", intensities=intensities, spotattr=data.frame(Name=I(rep(c("x","y","Blank","Blank","z"),20))), hybattr=NULL) res <- removeSpots(arrayDataObject, spotsToBeRemoved=c("x","z")) stopifnot( dim(getIntensities(res[["arrayDataObject"]]))[1] == 3*20 ) indCy3=1:3 indCy5=4:6 channels <- matrix( c(indCy3,indCy5), nrow=length(indCy3), byrow=FALSE ) colnames(channels) <- c("Cy3","Cy5") exprSetArrayObject <- new("exprSetArray", exprs=matrix(data=runif(600),nrow=100,ncol=6), phenoData=new("phenoData", pData=data.frame(matrix(0,nrow=6,ncol=1)), varLabels=list(rep("varLabel1",1))), channels=channels) res2 <- removeSpots(arrayDataObject=arrayDataObject,exprSetArrayObject=exprSetArrayObject, spotsToBeRemoved=c("x","z")) stopifnot( dim(exprs(res2[["exprSetArrayObject"]]))[1] == 3*20 ) res3 <- removeSpots(arrayDataObject=arrayDataObject,exprSetArrayObject=exprSetArrayObject, spotsToBeRemoved=c("ggrrrr")) stopifnot( dim(exprs(res3[["exprSetArrayObject"]]))[1] == 100 ) stopifnot( dim(getIntensities(res3[["arrayDataObject"]]))[1] == 100 )