R/expression.r

In BrainStars: query gene expression data and plots from BrainStars (B*)

.getBrainStarsExpression <- function(query) {
  api.name <- "probeset"
  res <- getBrainStars(query = query, type = api.name, json = TRUE)  
  url <- fromJSON(res)$file1d$csv["href"]

  expr <- read.csv(url, row.names=1)
  return(as.matrix(expr))
}
# Retreive a list of expression profile from BrainStars
#
# This function queries a list of gene expression profile from BrainStars
#
# @usage getBrainStarsExpression(queries)
# @param queries vector of Affymetrix GeneChip IDs (Mouse Genome 430 2.0 array)
# @return An object of ExpressionSet is returned.
# @importClassesFrom Biobase ExpressionSet
# @importMethodsFrom Biobase annotation exprs featureNames pData rowQ varLabels "featureNames<-" "sampleNames<-"
# @examples
# mk.genes <- getBrainStarsMarker("low/SCN/all")
# mk.ids   <- mk.genes[,1]
# mk.eset  <- getBrainStarsExpression(mk.ids)
getBrainStarsExpression <- function(queries) {

  expr <- .getBrainStarsExpression(queries[1])
  num.expr    <- ncol(expr)
  num.entries <- length(queries)
  
  expr.mat <- matrix(nrow = num.entries, ncol = num.expr)

  expr.mat[1,] <- expr
  sample.names <- colnames(expr)

  if (num.entries > 1 ) {
    for (i in 2:num.entries) {
      expr.mat[i,] <- .getBrainStarsExpression(queries[i])
    }
  }
  
  eset <- new("ExpressionSet", expr = expr.mat)
  featureNames(eset) <- queries
  sampleNames(eset)  <- sample.names
  
  return(eset)
}