@@ -2,7 +2,7 @@ Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for

         Affymetrix SNP 5.0 and 6.0 and Illumina arrays

-Version: 1.37.0

+Version: 1.37.1

 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo

         Ruczinski, Rafael A Irizarry

 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,

@@ -324,186 +324,139 @@ readGenCallOutput = function(filenames, path=".", cdfName,

-RGtoXY = function(RG, chipType, anno, verbose=TRUE) {

-  if(chipType!="nopackage") {

-  needToLoad <- !all(sapply(c('addressA', 'addressB', 'base'), isLoaded))

-  if(needToLoad){

-	  chipList = c("human1mv1c",# 1M

-	  "human370v1c",            # 370CNV

-	  "human650v3a",            # 650Y

-	  "human610quadv1b",        # 610 quad

-	  "human660quadv1a",        # 660 quad

-	  "human370quadv3c",        # 370CNV quad

-	  "human550v3b",            # 550K

-	  "human1mduov3b",          # 1M Duo

-	  "humanomni1quadv1b",      # Omni1 quad

-	  "humanomni25quadv1b",     # Omni2.5 quad

-	  "humanomni258v1a",        # Omni2.5 8 v1 A

-          "humanomni258v1p1b",      # Omni2.5 8 v1.1 B

-          "humanomni5quadv1b",      # Omni5 quad  

-	  "humanomniexpress12v1b",  # Omni express 12

-	  "humanimmuno12v1b",       # Immuno chip 12

-          "humancytosnp12v2p1h",    # CytoSNP 12

-          "humanexome12v1p2a",      # Exome 12 v1.2 A

-          "humanomniexpexome8v1p1b") # Omni Express Exome 8 v1.1b

-	  ## RS: added cleancdfname()

-	  if(missing(chipType)){

-		  chipType = match.arg(cleancdfname(annotation(RG)), chipList)

-	  } else chipType = match.arg(cleancdfname(chipType), chipList)

-	  pkgname = getCrlmmAnnotationName(chipType)

-	  if(!require(pkgname, character.only=TRUE, quietly=!verbose)){

-		  suggCall = paste("library(", pkgname, ", lib.loc='/Altern/Lib/Loc')", sep="")

-		  msg = paste("If", pkgname, "is installed on an alternative location, please load it manually by using", suggCall)

-		  message(strwrap(msg))

-		  stop("Package ", pkgname, " could not be found.")

-		  rm(suggCall, msg)

-	  }

-	  if(verbose) message("Loading chip annotation information.")

-	  loader("address.rda", .crlmmPkgEnv, pkgname)

-  }

-  aids = getVarInEnv("addressA") # comes from AddressA_ID or Address column in manifest

-  bids = getVarInEnv("addressB") # comes from AddressB_ID or Address2 column in manifest

-  snpbase = getVarInEnv("base")

-##  loader(‘file.rda’)

-##  x = getVarInEnv(‘x’)

-##  y = getVarInEnv(‘y’)

-##

-##  I’d consider using something like:

-##

-##	  needToLoad = !all(sapply(c(‘x’, ‘y’), isLoaded))

-##  if (needToLoad){

-##	  loader(‘file.rda’)

-##	  x = getVarInEnv(‘x’)

-##	  y = getVarInEnv(‘y’)

-##  }

-  ids = names(aids)

-  nsnps = length(aids)

-  narrays = ncol(RG)

-#  aidcol = match("AddressA_ID", colnames(annot))

-#  if(is.na(aidcol))

-#    aidcol = match("Address", colnames(annot))

-#  if(is.na(bidcol))

-#    bidcol = match("Address2", colnames(annot))

-#  aids = annot[, aidcol]

-#  bids = annot[, bidcol]

-#  snpids = annot[,"Name"]

-#  snpbase = annot[,"SNP"]

-  infI = !is.na(bids) & bids!=0

-  aord = match(aids, featureNames(RG)) # NAs are possible here

-  bord = match(bids, featureNames(RG)) # and here

-#  argrg = aids[rrgg]

-#  brgrg = bids[rrgg]

-  xyPhenoData = AnnotatedDataFrame(data=RG@phenoData@data,varMetadata=RG@phenoData@varMetadata)

-  levels(xyPhenoData@varMetadata$channel) = c("X","Y","zero","_ALL_")

-  XY <- new("NChannelSet",

-        assayDataNew(X=initializeBigMatrix(name="X", nr=nsnps, nc=narrays, vmode="integer"),

-                     Y=initializeBigMatrix(name="Y", nr=nsnps, nc=narrays, vmode="integer"),

-                     zero=initializeBigMatrix(name="zero", nr=nsnps, nc=narrays, vmode="integer")),

-        phenoData=xyPhenoData, protocolData=RG@protocolData, annotation=chipType)

-   storageMode(XY) = "environment"

-#  XY <- new("NChannelSet",

-#	    X=matrix(0, nsnps, narrays),

-#	    Y=matrix(0, nsnps, narrays),

-#	    zero=matrix(0, nsnps, narrays),

-#	    annotation=chipType, phenoData=RG@phenoData,

-#	    protocolData=RG@protocolData, storage.mode="environment")

-  featureNames(XY) = ids

-  sampleNames(XY) = sampleNames(RG)

-  ## RS

-  rm(list=c("bord", "infI", "aids", "bids", "ids", "snpbase"))

-#  print(gc())

-  gc(verbose=FALSE)

-  # Need to initialize - matrices filled with NAs to begin with

-#  XY@assayData$X[1:nsnps,] = 0

-#  XY@assayData$Y[1:nsnps,] = 0

-#  XY@assayData$zero[1:nsnps,] = 0

-

-  # First sort out Infinium II SNPs, X -> R (allele A)  and Y -> G (allele B) from the same probe

-  ## RS added

-  not.na <- !is.na(aord)

-  not.na.aord <- aord[not.na]

-  ## RS substitution  !is.na(aord) -> not.na

-  ##r <- as.matrix(exprs(channel(RG, "R"))[not.na.aord,]) # mostly red

-  r <- as.matrix(assayData(RG)[["R"]][not.na.aord, ])

-  XY@assayData$X[not.na,] <- r

-  rm(r);gc(verbose=FALSE)

-  g <- as.matrix(assayData(RG)[["G"]][not.na.aord,]) # mostly green

-  XY@assayData$Y[not.na,] <- g

-  rm(g); gc(verbose=FALSE)

-  ##z <- as.matrix(exprs(channel(RG, "zero"))[not.na.aord,]) # mostly green

-  z <- as.matrix(assayData(RG)[["zero"]][not.na.aord, ])

-  XY@assayData$zero[not.na,] <- z

-  rm(z); gc(verbose=FALSE)

-  ##RS added

-  rm(RG)

-#  print(gc())

-  gc(verbose=FALSE)

-  ## Warning - not 100% sure that the code below is correct - could be more complicated than this

-#  infIRR = infI & (snpbase=="[A/T]" | snpbase=="[T/A]" | snpbase=="[a/t]" | snpbase=="[t/a]")

-

-#  X[infIRR,] = exprs(channel(RG, "R"))[aord[infIRR],] # mostly red

-#  Y[infIRR,] = exprs(channel(RG, "R"))[bord[infIRR],] # mostly green

-

-  # Finally Infinium I where X -> G from allele A probe and Y -> G from allele B probe

-#  infIGG = infI & (snpbase=="[C/G]" | snpbase=="[G/C]" | snpbase=="[g/c]" | snpbase=="[c/g]")

-

-#  X[infIGG,] = exprs(channel(RG, "G"))[aord[infIGG],] # mostly red

-#  Y[infIGG,] = exprs(channel(RG, "G"))[bord[infIGG],] # mostly green

+RGtoXY = function (RG, chipType, anno, verbose = TRUE) 

+{

+    if (chipType != "nopackage") {

+        needToLoad <- !all(sapply(c("addressA", "addressB", "base"), 

+            isLoaded))

+        if (needToLoad) {

+            chipList = c("human1mv1c", "human370v1c", "human650v3a", 

+                "human610quadv1b", "human660quadv1a", "human370quadv3c", 

+                "human550v3b", "human1mduov3b", "humanomni1quadv1b", 

+                "humanomni25quadv1b", "humanomni258v1a", "humanomni258v1p1b", 

+                "humanomni5quadv1b", "humanomniexpress12v1b", 

+                "humanimmuno12v1b", "humancytosnp12v2p1h", "humanexome12v1p2a", 

+                "humanomniexpexome8v1p1b")

+            if (missing(chipType)) {

+                chipType = match.arg(cleancdfname(annotation(RG)), 

+                  chipList)

+            }

+            else chipType = match.arg(cleancdfname(chipType), 

+                chipList)

+            pkgname = getCrlmmAnnotationName(chipType)

+            if (!require(pkgname, character.only = TRUE, quietly = !verbose)) {

+                suggCall = paste("library(", pkgname, ", lib.loc='/Altern/Lib/Loc')", 

+                  sep = "")

+                msg = paste("If", pkgname, "is installed on an alternative location, please load it manually by using", 

+                  suggCall)

+                message(strwrap(msg))

+                stop("Package ", pkgname, " could not be found.")

+                rm(suggCall, msg)

+            }

+            if (verbose) 

+                message("Loading chip annotation information.")

+            loader("address.rda", .crlmmPkgEnv, pkgname)

+        }

+        aids = getVarInEnv("addressA")

+        bids = getVarInEnv("addressB")

+        snpbase = getVarInEnv("base")

+        ids = names(aids)

+        nsnps = length(aids)

+        narrays = ncol(RG)

+        infI = !is.na(bids) & bids != 0

+        aord = match(aids, featureNames(RG))

+        bord = match(bids, featureNames(RG))

+        xyPhenoData = AnnotatedDataFrame(data = RG@phenoData@data, 

+            varMetadata = RG@phenoData@varMetadata)

+        levels(xyPhenoData@varMetadata$channel) = c("X", "Y", 

+            "zero", "_ALL_")

+        XY <- new("NChannelSet", assayDataNew(X = initializeBigMatrix(name = "X", 

+            nr = nsnps, nc = narrays, vmode = "integer"), Y = initializeBigMatrix(name = "Y", 

+            nr = nsnps, nc = narrays, vmode = "integer"), zero = initializeBigMatrix(name = "zero", 

+            nr = nsnps, nc = narrays, vmode = "integer")), phenoData = xyPhenoData, 

+            protocolData = RG@protocolData, annotation = chipType)

+        storageMode(XY) = "environment"

+        featureNames(XY) = ids

+        sampleNames(XY) = sampleNames(RG)

+        rm(list = c("bord", "infI", "aids", "bids", "ids", "snpbase"))

+        gc(verbose = FALSE)

+        not.na <- !is.na(aord)

+        not.na.aord <- aord[not.na]

+        r <- as.matrix(assayData(RG)[["R"]][not.na.aord, ])

+        XY@assayData$X[not.na, ] <- r

+        rm(r)

+        gc(verbose = FALSE)

+        g <- as.matrix(assayData(RG)[["G"]][not.na.aord, ])

+        XY@assayData$Y[not.na, ] <- g

+        rm(g)

+        gc(verbose = FALSE)

+        z <- as.matrix(assayData(RG)[["zero"]][not.na.aord, ])

+        XY@assayData$zero[not.na, ] <- z

+        rm(z)

+        gc(verbose = FALSE)

+        rm(RG)

+        gc(verbose = FALSE)

+    }

+    if (chipType == "nopackage" && !is.null(anno)) {

+        pkgname = NULL

+        if(sum(colnames(anno@data)=="AddressA_ID")!=1){

+           

+           message("annotation format is wrong, could not find a column with name: AddressA_ID")

+         }else{

+         anno2=anno@data

+           # chr = as.character(anno$Chr)

+  #chr[chr=="X"] = 23

+  #  chr[chr=="Y"] = 24

+  #  chr[chr=="XY"] = 25

+#chr[chr=="MT"] = 26

+#anno[,"chromosome"]=as.integer(chr)

-  #  For now zero out Infinium I probes

-#  XY@assayData$X[infI,] = 0

-#  XY@assayData$Y[infI,] = 0

-#  XY@assayData$zero[infI,] = 0

-#  gc(verbose=FALSE)

-  }

-  if(chipType=="nopackage" && !is.null(anno)) {

-            pkgname=NULL

-#            anno=read.csv(annot,header=TRUE, as.is=TRUE, check.names=FALSE,skip=7)

-            aids=anno[,"AddressA_ID"]

-            bids=anno[,"AddressB_ID"]

-            snpbase=anno[,"SNP"]

-            names(aids)=ids=anno[,"Name"]

-#            m=match(aids,rownames(RG@assayData$R))

-#            ARG=RG[m[!is.na(m)],]

-#            mm=match(rownames(ARG@assayData$R),aids)

-#            aids=aids[mm]

-#            bids=bids[mm]

-#            snpbas=snpbase[mm]

-            nsnps = length(aids)

-            narrays = ncol(RG)

-            infI = !is.na(bids) & bids != 0

-            aord = match(aids, featureNames(RG))

-            bord = match(bids, featureNames(RG))

-            xyPhenoData = AnnotatedDataFrame(data = RG@phenoData@data, 

-                                             varMetadata = RG@phenoData@varMetadata)

-            levels(xyPhenoData@varMetadata$channel) = c("X", "Y", "zero", "_ALL_")

-            XY <- new("NChannelSet", assayDataNew(X = initializeBigMatrix(name="X", nr=nsnps, nc=narrays, vmode="integer"),

-                                                  Y = initializeBigMatrix(name="Y", nr=nsnps, nc=narrays, vmode="integer"),

-                                                  zero = initializeBigMatrix(name="zero", nr=nsnps, nc=narrays, vmode="integer")),

-                      phenoData = xyPhenoData, protocolData = RG@protocolData)

-            storageMode(XY) = "environment"

-            featureNames(XY) = names(aids)

-            sampleNames(XY) = sampleNames(RG)

-            rm(list = c("bord", "infI", "aids", "bids", "snpbase"))

-            gc(verbose = FALSE)

-            not.na <- !is.na(aord)

-            not.na.aord <- aord[not.na]

-            r <- as.matrix(assayData(RG)[["R"]][not.na.aord, ])

-            XY@assayData$X[not.na, ] <- r

-            rm(r)

-            gc(verbose = FALSE)

-            g <- as.matrix(assayData(RG)[["G"]][not.na.aord, ])

-            XY@assayData$Y[not.na, ] <- g

-            rm(g)

-            gc(verbose = FALSE)

-            z <- as.matrix(assayData(RG)[["zero"]][not.na.aord, ])

-            XY@assayData$zero[not.na, ] <- z

-            rm(z)

-            gc(verbose = FALSE)

-            rm(RG)

-            gc(verbose = FALSE)

-   }

-   XY

+       aids = anno2[, "AddressA_ID"]

+        bids = anno2[, "AddressB_ID"]

+        snpbase = anno2[, "SNP"]

+        names(aids) = ids = anno2[, "featureNames"]

+        nsnps = length(aids)

+        narrays = ncol(RG)

+        infI = !is.na(bids) & bids != 0

+        aord = match(aids, featureNames(RG))

+        bord = match(bids,featureNames(RG))

+        xyPhenoData = AnnotatedDataFrame(data = RG@phenoData@data, 

+            varMetadata = RG@phenoData@varMetadata)

+        levels(xyPhenoData@varMetadata$channel) = c("X", "Y", 

+            "zero", "_ALL_")

+        XY <- new("NChannelSet", assayDataNew(X = initializeBigMatrix(name = "X", 

+            nr = nsnps, nc = narrays, vmode = "integer"), Y = initializeBigMatrix(name = "Y", 

+            nr = nsnps, nc = narrays, vmode = "integer"), zero = initializeBigMatrix(name = "zero", 

+            nr = nsnps, nc = narrays, vmode = "integer")), phenoData = xyPhenoData, 

+            protocolData = RG@protocolData)

+        storageMode(XY) = "environment"

+       # featureNames(XY) = names(aids)

+        sampleNames(XY) = sampleNames(RG)

+        rm(list = c("bord", "infI", "aids", "bids", "snpbase"))

+        gc(verbose = FALSE)

+        not.na <- !is.na(aord)

+        not.na.aord <- aord[not.na]

+        r <- as.matrix(assayData(RG)[["R"]][not.na.aord, ])

+        XY@assayData$X[not.na, ] <- r

+        rm(r)

+        gc(verbose = FALSE)

+        g <- as.matrix(assayData(RG)[["G"]][not.na.aord, ])

+        XY@assayData$Y[not.na, ] <- g

+        rm(g)

+        gc(verbose = FALSE)

+        z <- as.matrix(assayData(RG)[["zero"]][not.na.aord, ])

+        XY@assayData$zero[not.na, ] <- z

+        rm(z)

+        gc(verbose = FALSE)

+        rm(RG)

+        gc(verbose = FALSE)

+   

+    

+    

+    

+         }

+      }

+           XY 

 }

@@ -1155,7 +1108,10 @@ constructInf <- function(sampleSheet=NULL,

             genome <- getAvailableIlluminaGenomeBuild(path)

             featureData = getFeatureData(cdfName, copynumber=TRUE, genome=genome)

           } else {

-            featureData=anno

+                      anno = as(anno, "AnnotatedDataFrame")

+ anno = as(anno, "GenomeAnnotatedDataFrame")

+featureData=anno

+           

           }

           nr <- nrow(featureData)

           nc <- narrays

@@ -144,7 +144,11 @@ priormeans=prepriormeans

     XIndex = seq(1:nrow(cnSet))[chromosome(cnSet)==23 & isSnp(cnSet)]

 ### impute gender if gender information not provided

     if (is.null(gender)) {

-       gender = krlmmImputeGender(cnSet, annotation, YIndex, verbose, offset=offset)

+       if(sum(is.na(YIndex))==length(YIndex)){

+		gender=NULL

+       }else{

+	gender = krlmmImputeGender(cnSet, annotation, YIndex, verbose, offset=offset)

+       }

     }

 ### double-check ChrY ChrX SNP cluster, impute gender if gender information not provided