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

 Package: crlmm

 Type: Package

 Title: Genotype Calling via CRLMM Algorithm

-Version: 1.0.36

+Version: 1.0.37

 Date: 2008-12-28

 Author: Rafael A Irizarry

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

@@ -17,5 +17,7 @@ Collate: crlmmGT.R

          zzz.R

          crlmmGTnm.R

          crlmmnm.R

+         AllClasses.R

+         Methods.R

 	 functions.R

 LazyLoad: yes

@@ -1,9 +1,11 @@

 useDynLib("crlmm", .registration=TRUE)

 export("crlmm", "list.celfiles", "computeCnBatch")

+exportMethods("list2crlmmSet", "calls", "confs")

+exportClasses("crlmmSet")

 importFrom(affyio, read.celfile.header, read.celfile)

 importFrom(preprocessCore, normalize.quantiles.use.target)

 importFrom(utils, data, packageDescription, setTxtProgressBar, txtProgressBar)

 importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd)

-##RS

 importFrom(Biobase, rowMedians)

 importFrom(genefilter, rowSds)

+

new file mode 100644

@@ -0,0 +1,2 @@

+## Class definition

+setClass("crlmmSet", contains="eSet")

new file mode 100644

@@ -0,0 +1,27 @@

+## Methods for crlmm

+

+setGeneric("calls", function(x) standardGeneric("calls"))

+setMethod("calls", "crlmmSet", function(x) assayData(x)$calls)

+

+setGeneric("confs", function(x) standardGeneric("confs"))

+setMethod("confs", "crlmmSet", function(x) assayData(x)$confs)

+

+setGeneric("list2crlmmSet", function(x) standardGeneric("list2crlmmSet"))

+setMethod("list2crlmmSet", "list",

+          function(x){

+            pd <- data.frame(SNR=x[["SNR"]],

+                             row.names=colnames(x[["calls"]]))

+            pdv <- data.frame(labelDescription=c("Signal-to-noise Ratio"),

+                              row.names=c("SNR"))

+            fd <- data.frame(SNPQC=x[["SNPQC"]],

+                             row.names=rownames(x[["calls"]]))

+            fdv <- data.frame(labelDescription=c("SNP Quality Score"),

+                              row.names=c("SNPQC"))

+            new("crlmmSet",

+                assayData=assayDataNew("lockedEnvironment",

+                  calls=x[["calls"]], confs=x[["confs"]]),

+                phenoData=new("AnnotatedDataFrame",

+                  data=pd, varMetadata=pdv),

+                featureData=new("AnnotatedDataFrame",

+                  data=fd, varMetadata=fdv))

+          })

@@ -158,10 +158,14 @@ crlmmGT <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

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

 ##     tmpSnpQc <- dev[autosomeIndex]

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

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

+    tmp4batchQC <- DD[snps2keep,]/(params[["N"]][snps2keep,]+1)

     tmpSnpQc <- dev[snps2keep]

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

-    batchQC <- mean(diag(SS))

+    SS <- cov(DD[snps2keep,])

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

+##     tmpSnpQc <- dev[snps2keep]

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

+    batchQC <- sqrt(sum(diag(cov(tmp4batchQC[tmpSnpQc < badSNP,]))))*sum(params[["N"]][snps2keep[1],])

+##    batchQC <- mean(diag(SS))

   }else{

     SS <- matrix(0, 3, 3)

     batchQC <- Inf

@@ -169,9 +173,9 @@ crlmmGT <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

   if(verbose) message("Done.")

   if (returnParams){

-    return(list(calls=A, confs=B, SNPQC=dev, batchQC=batchQC, params=params, DD=DD, covSS=SS))

+    return(list(calls=A, confs=B, SNPQC=dev, batchQC=batchQC, params=params, DD=DD, covDD=SS))

   }else{

-    return(list(calls=A, confs=B, SNPQC=dev, batchQC=batchQC, DD=DD, covSS=SS))

+    return(list(calls=A, confs=B, SNPQC=dev, batchQC=batchQC, DD=DD, covDD=SS))

   }

 }

@@ -225,7 +229,7 @@ gtypeCallerR2 <- function(A, B, fIndex, mIndex, theCenters, theScales,

 ##################

 ##################

-### THIS IS TEMPORARY NOT OFFICIALLY USED

+### THIS IS TEMPORARY AND NOT OFFICIALLY USED

 ##################

 ####################

 crlmmGTTNoN <- function(A, B, SNR, mixtureParams, cdfName,

Binary files a/inst/doc/crlmm.pdf and b/inst/doc/crlmm.pdf differ