@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling via CRLMM Algorithm

-Version: 1.0.30

+Version: 1.0.31

 Date: 2008-12-28

 Author: Rafael A Irizarry

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>

@@ -104,11 +104,14 @@ crlmmGT <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

       noMoveIndex <- union(setdiff(which(rowSums(is.na(newparams[["centers"]]))>0), YIndex), 

                            YIndex[rowSums(is.na(newparams[["centers"]][YIndex, ])>1)])

     }

+    snps2ignore <- which(rowSums(is.na(newparams[["centers"]])) > 0)

+    snps2keep <- setdiff(autosomeIndex, snps2ignore)

+    rm(snps2ignore)

     newparams[["centers"]][is.na(newparams[["centers"]])] <- params[["centers"]][is.na(newparams[["centers"]])]

     if(verbose) cat("\n")

     if(verbose) message("Calculating and standardizing size of shift.")

-    DD <- newparams[["centers"]] - params[["centers"]]

+    GG <- DD <- newparams[["centers"]] - params[["centers"]]

     DD <- sweep(DD, 2, colMeans(DD[autosomeIndex, ]))

     SS <- cov(DD[autosomeIndex, ])

     SSI <- solve(SS)

@@ -150,9 +153,12 @@ crlmmGT <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

   if(!is.null(col.names)){ colnames(A) <- colnames(B) <- col.names}

   if(length(Index) >= recallRegMin){

-    tmp4batchQC <- DD[autosomeIndex,]/(params[["N"]][autosomeIndex,]+1)

-    tmpSnpQc <- dev[autosomeIndex]

-    SS <- cov(tmp4batchQC[tmpSnpQc < badSNP,])

+##     tmp4batchQC <- DD[autosomeIndex,]/(params[["N"]][autosomeIndex,]+1)

+##     tmpSnpQc <- dev[autosomeIndex]

+##     SS <- cov(tmp4batchQC[tmpSnpQc < badSNP,])

+    DD <- sweep(GG[snps2keep, ], 2, colMeans(DD[snps2keep, ]))

+    tmpSnpQc <- dev[snps2keep]

+    SS <- cov(DD[tmpSnpQc < badSNP, ])

     batchQC <- mean(diag(SS))

   }else{

     batchQC <- Inf

@@ -6,6 +6,11 @@ SEXP gtypeCallerPart1nm(SEXP *, SEXP *, SEXP *, SEXP *, SEXP *,SEXP *, SEXP *,

 		        SEXP *, SEXP *, SEXP *, SEXP *, SEXP *,SEXP *, SEXP *,

                         SEXP *, SEXP *, SEXP *);

+SEXP gtypeCallerPart2nm(SEXP *, SEXP *, SEXP *, SEXP *,

+		      SEXP *, SEXP *, SEXP *, SEXP *,

+                      SEXP *, SEXP *, SEXP *, SEXP *,

+		      SEXP *, SEXP *, SEXP *, SEXP *,

+                      SEXP *, SEXP *, SEXP *);

 SEXP test (SEXP *);

@@ -13,6 +18,17 @@ SEXP gtypeCallerPart1NormalNoN(SEXP *, SEXP *, SEXP *, SEXP *,SEXP *, SEXP *,

                                SEXP *, SEXP *, SEXP *, SEXP *,SEXP *, SEXP *,

 		               SEXP *, SEXP *, SEXP *, SEXP *,SEXP *);

+SEXP gtypeCallerPart2NormalNoN(SEXP *, SEXP *, SEXP *, SEXP *,

+		      SEXP *, SEXP *, SEXP *, SEXP *,

+                      SEXP *, SEXP *, SEXP *, SEXP *,

+		      SEXP *, SEXP *, SEXP *, SEXP *,

+                      SEXP *, SEXP *, SEXP *);

+

+

+SEXP gtypeCallerPart1(SEXP *, SEXP *, SEXP *, SEXP *,SEXP *, SEXP *,

+		      SEXP *, SEXP *, SEXP *, SEXP *,SEXP *, SEXP *,

+		      SEXP *, SEXP *, SEXP *, SEXP *,SEXP *);

+

 SEXP gtypeCallerPart2(SEXP *, SEXP *, SEXP *, SEXP *,

 		      SEXP *, SEXP *, SEXP *, SEXP *,

                       SEXP *, SEXP *, SEXP *, SEXP *,

@@ -23,11 +39,11 @@ SEXP gtypeCallerPart1TNoN(SEXP *, SEXP *, SEXP *, SEXP *,

 		          SEXP *, SEXP *, SEXP *, SEXP *,

                           SEXP *, SEXP *, SEXP *, SEXP *,

 		          SEXP *, SEXP *, SEXP *,

-		      SEXP *, SEXP *)

+			  SEXP *, SEXP *);

 SEXP gtypeCallerPart2TNoN(SEXP *, SEXP *, SEXP *, SEXP *,

 			  SEXP *, SEXP *, SEXP *, SEXP *, 

 			  SEXP *, SEXP *, SEXP *, SEXP *,

 			  SEXP *, SEXP *, SEXP *, SEXP *,

-			  SEXP *, SEXP *, SEXP *)

\ No newline at end of file

+			  SEXP *, SEXP *, SEXP *);

@@ -14,8 +14,7 @@ static const R_CallMethodDef CallEntries[] = {

     {NULL, NULL, 0}

 };

-void R_init_crlmm(DllInfo *dll)

-{

+void R_init_crlmm(DllInfo *dll){

     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);    

 }