##
# mae.readVSfile(file) - read vertically stacked array expression data
# Args: file is the data file name
# Value: data frame with
#    vData         - data frame of vertically stacked data
#    sampleNames   - sample names
#    condNames     - unique condition names
#    allCondNames  - condition names for each sample (factor)
#    nSamples      - # of samples
#    nConds        - # of conditions
#    nGenes        - # of nGenes 
#    isVertStacked - TRUE 
#
# Developer: P. Lemkin, G. Thornwall
# Date: 6/10/2003
##
mae.readVSfile <- function(file)
{ # readVSfile
  vData <- read.table(file, header=TRUE)
  allSampleNames <- factor(vData$sampleName)
  allCondNames <- factor(vData$condName)
  sampleNames <- unique(allSampleNames)
  condNames <- unique(allCondNames)
  nSamples <- length(allSampleNames)
  nConds <- length(condNames)
  nGenes <- sum(vData$sampleName==sampleNames[1])
  return(vData=vData,sampleNames=sampleNames,condNames=condNames,
         allCondNames=allCondNames,nSamples=nSamples,nConds=nConds,
         nGenes=nGenes,isVertStacked=TRUE)
} # end of mae.readVSfile