I had broken generate.celltype.data while trying to make it run faste…

…r. It was just summing reads instead of calculating their mean. Fixed. Thanks to Kaitlyn Price of Toronto for spotting the bug!

Former-commit-id: 7ded1d0

R/generate.celltype.data.r

@@ -62,10 +62,16 @@ generate.celltype.data <- function(exp,annotLevels,groupName,no_cores=1,savePath
             }
             ctd_oneLevel$mean_exp = as.matrix(expMatrix)
         }else{
+            # Sum reads in each cell type
             #mean_exp = apply(expMatrix,1,aggregate.over.celltypes,ctd_oneLevel$annot)
             mm <- model.matrix(~ 0 + ctd_oneLevel$annot)
             colnames(mm) <- names(table(ctd_oneLevel$annot))
             mat.summary.mm1 <- expMatrix %*% mm
+
+            # Divide by the number of cells to get the mean
+            cellCounts = table(ctd_oneLevel$annot)
+            for(i in 1:dim(mat.summary.mm1)[2]){mat.summary.mm1[,i] = mat.summary.mm1[,i]/cellCounts[i]}
+
             ctd_oneLevel$mean_exp = as.matrix(mat.summary.mm1)
         }
         return(ctd_oneLevel)