@@ -761,16 +761,13 @@ crlmmCopynumberLD <- function(object,

 		 neededPkgs="crlmm")

 	return(object)

 }

-crlmmCopynumber <- crlmmCopynumber2 <- crlmmCopynumberLD

+yycrlmmCopynumber2 <- crlmmCopynumberLD

 fit.lm1 <- function(idxBatch,

 		    snpBatches,

-##		    autosomeIndex,

 		    marker.index,

 		    object,

 		    Ns,

-##		    normal,

-##		    snpflags,

 		    batchSize,

 		    SNRMin,

 		    MIN.SAMPLES,

@@ -977,8 +974,6 @@ fit.lm2 <- function(idxBatch,

 		    marker.index,

 		    object,

 		    Ns,

-##		    normal,

-##		    snpflags,

 		    batchSize,

 		    SNRMin,

 		    MIN.SAMPLES,

@@ -1088,8 +1083,6 @@ fit.lm3 <- function(idxBatch,

 		    marker.index,

 		    object,

 		    Ns,

-##		    normal,

-##		    snpflags,

 		    batchSize,

 		    SNRMin,

 		    MIN.SAMPLES,

@@ -1327,8 +1320,6 @@ fit.lm4 <- function(idxBatch,

 		    marker.index,

 		    object,

 		    Ns,

-##		    normal,

-##		    snpflags,

 		    batchSize,

 		    SNRMin,

 		    MIN.SAMPLES,

@@ -2774,9 +2765,9 @@ ellipseCenters <- function(object, index, allele, batch, log.it=TRUE){

 }

-computeCN <- function(object,

-		      filenames,

-		      which.batches,

+crlmmCopynumber <- function(object,

+			    filenames,

+			    which.batches,

 		      MIN.SAMPLES=10,

 		      SNRMin=5,

 		      MIN.OBS=1,