Merge pull request jtleek#1 from wevanjohnson/master

Added a long overdue error message to ComBat when the experimental design is confounded

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sva
 Title: Surrogate Variable Analysis
-Version: 3.13.0
+Version: 3.13.1
 Author: Jeffrey T. Leek <jtleek@gmail.com>, W. Evan Johnson <wej@bu.edu>,
     Hilary S. Parker <hiparker@jhsph.edu>, Elana J. Fertig <ejfertig@jhmi.edu>,
     Andrew E. Jaffe <ajaffe@jhsph.edu>, John D. Storey <jstorey@princeton.edu>

R/ComBat.R

@@ -36,6 +36,15 @@ ComBat <- function(dat, batch, mod, numCovs = NULL, par.prior=TRUE,prior.plots=F
   n.batches <- sapply(batches, length)
   n.array <- sum(n.batches)
 
+  # Checking if the design is confounded
+  if(qr(design)$rank<ncol(design)){
+    if(ncol(design)<=(n.batch)){stop("your batch variables are redundant or nested! Please remove one or more of the batch variables so they are no longer confounded.")}
+    if(ncol(design)==(n.batch+1)){stop("your covariate is confounded with batch! Please remove the confounded covariate and rerun ComBat.")}
+    if(ncol(design)>(n.batch+1)){
+      if((qr(design[,-c(1:n.batch)])$rank<ncol(design[,-c(1:n.batch)]))){stop('the experimental design of your covariates is confounded! Please remove one (or more) of the covariates so that your design is no longer confounded.')
+      }else{stop("one (or more) of your covariates is confounded with batch! Please remove the confounded covariate and rerun ComBat.")}}
+  }
+
   ## Check for missing values
   NAs = any(is.na(dat))
   if(NAs){cat(c('Found',sum(is.na(dat)),'Missing Data Values\n'),sep=' ')}