@@ -137,3 +137,9 @@ is decoded and scanned

 2009-04-08 Matt Ritchie - committed version 1.0.79

 * fixed bug in readIDAT and readIdatFiles from reading in RunInfo header information

+

+2009-04-07 B Carvalho - committed version 1.0.80 (advantages of being a lot of hours behind)

+

+* Fixed downstream vignette to account for the SnpSet object being returned by crlmm

+

+* Fixed some minor status messages

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

 Package: crlmm

 Type: Package

-Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays.

-Version: 1.0.79

+Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

+Version: 1.0.80

 Date: 2008-12-30

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -100,7 +100,7 @@ crlmmGT <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

                    keepIndex[which(gender[keepIndex]==2)], 

                    keepIndex[which(gender[keepIndex]==1)])

-  if(verbose) cat("Calling", NR, "SNPs for recalibration")

+  if(verbose) cat("Calling", NR, "SNPs for recalibration... ")

   ## call C

   fIndex <- which(gender==2)

@@ -185,7 +185,7 @@ crlmmGT <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

   params[-2] <- newparams[-2]

   rm(newparams);gc(verbose=FALSE)  

-  if(verbose) cat("Calling", NR, "SNPs")

+  if(verbose) cat("Calling", NR, "SNPs... ")

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

   ## ## MOVE TO C#######

   ImNull <- gtypeCallerR2(A, B, fIndex, mIndex, params[["centers"]],

@@ -426,7 +426,7 @@ crlmmGTTNoN <- function(A, B, SNR, mixtureParams, cdfName,

                    keepIndex[which(gender[keepIndex]==2)], 

                    keepIndex[which(gender[keepIndex]==1)])

-  if(verbose) cat("Calling", NR, "SNPs for recalibration")

+  if(verbose) cat("Calling", NR, "SNPs for recalibration... ")

   ## call C

   fIndex <- which(gender==2)

@@ -498,7 +498,7 @@ crlmmGTTNoN <- function(A, B, SNR, mixtureParams, cdfName,

   ## BC: must keep SD

   params[-2] <- newparams[-2]

   rm(newparams);gc(verbose=FALSE)  

-  if(verbose) cat("Calling", NR, "SNPs")

+  if(verbose) cat("Calling", NR, "SNPs... ")

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

   ## ## MOVE TO C#######

   t0 <- proc.time()

@@ -592,7 +592,7 @@ crlmmGTNormalNoN <- function(A, B, SNR, mixtureParams, cdfName,

                    keepIndex[which(gender[keepIndex]==2)], 

                    keepIndex[which(gender[keepIndex]==1)])

-  if(verbose) cat("Calling", NR, "SNPs for recalibration")

+  if(verbose) cat("Calling", NR, "SNPs for recalibration... ")

   ## call C

   fIndex <- which(gender==2)

@@ -664,7 +664,7 @@ crlmmGTNormalNoN <- function(A, B, SNR, mixtureParams, cdfName,

   ## BC: must keep SD

   params[-2] <- newparams[-2]

   rm(newparams);gc(verbose=FALSE)  

-  if(verbose) cat("Calling", NR, "SNPs")

+  if(verbose) cat("Calling", NR, "SNPs... ")

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

   ## ## MOVE TO C#######

   t0 <- proc.time()

@@ -773,7 +773,7 @@ crlmmGTnm <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

                    keepIndex[which(gender[keepIndex]==2)], 

                    keepIndex[which(gender[keepIndex]==1)])

-  if(verbose) cat("Calling", NR, "SNPs for recalibration")

+  if(verbose) cat("Calling", NR, "SNPs for recalibration... ")

   ## call C

   fIndex <- which(gender==2)

@@ -858,7 +858,7 @@ crlmmGTnm <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

   params[-2] <- newparams[-2]

   rm(newparams);gc(verbose=FALSE)  

-  if(verbose) cat("Calling", NR, "SNPs")

+  if(verbose) cat("Calling", NR, "SNPs... ")

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

   ## ## MOVE TO C#######

   t0 <- proc.time()

@@ -1,7 +1,6 @@

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

 ### FOR CRLMM

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

-- Fix downstream vignette

 - Add RS ids to annotation packages

 - Allele plots

 - M v S plots

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

@@ -57,14 +57,12 @@ if (!exists("crlmmResult")) {

 }

 @

-This is currently a list.

+This is currently a \Rclass{SnpSet} object.

 <<lkj21>>=

   class(crlmmResult)

-  sapply(crlmmResult, dim)

-  sapply(crlmmResult, length)

 @

-\section{Constructing an eSet extension}

+\section{Adding information to a \Rclass{SnpSet}}

 We will use the \Rpackage{GGdata} package to obtain extra information

 on the samples. This will be later used when building an \Rclass{eSet}

@@ -74,30 +72,27 @@ extension to store the genotyping results.

   if (!exists("hmceuB36")) data(hmceuB36)

   pd <- phenoData(hmceuB36)

   ggn <- sampleNames(pd)

-  preSN <- colnames(crlmmResult[["calls"]])

+  preSN <- sampleNames(crlmmResult)

   simpSN <- gsub("_.*", "", preSN)

   if (!all.equal(simpSN, ggn)) stop("align GGdata phenoData with crlmmResult read")

 @ 

-The list obtained as output of the \Rmethod{crlmm} method can be

-easily coerced to an eSet extension with the help of the helper

-function \Rfunction{list2crlmmSet}.

+The additional information obtained from \Rpackage{GGdata} can be

+easily combined to what is already available on \Robject{crlmmResult}.

 <<docl>>=

-  colnames(crlmmResult[["calls"]]) <- colnames(crlmmResult[["confs"]]) <- simpSN

-  crlmmResultSet <- list2crlmmSet(crlmmResult)

-  phenoData(crlmmResultSet) <- combine(pd, phenoData(crlmmResultSet))

-  crlmmResultSet

-  dim(calls(crlmmResultSet))

-  dim(confs(crlmmResultSet))

-  calls(crlmmResultSet)[1:10, 1:2]

-  confs(crlmmResultSet)[1:10, 1:2]

+  sampleNames(crlmmResult) <- simpSN

+  phenoData(crlmmResult) <- combine(pd, phenoData(crlmmResult))

+  dim(calls(crlmmResult))

+  dim(confs(crlmmResult))

+  calls(crlmmResult)[1:10, 1:2]

+  confs(crlmmResult)[1:10, 1:2]

 @

 \section{Coercing to snp.matrix as a prelude to a GWAS}

 <<lksnm>>=

 library(snpMatrix)

-crlmmSM <- as(t(calls(crlmmResultSet))-1, "snp.matrix")

+crlmmSM <- as(t(calls(crlmmResult))-1, "snp.matrix")

 crlmmSM

 @

@@ -116,12 +111,15 @@ gwas <- snp.rhs.tests(ex~male, data=subjdata, snp.data=crlmmSM, family="gaussian

 ok <- which(p.value(gwas) < 1e-10)

 gwas[ok,]

 <<dopl,fig=TRUE>>=

-plot(ex~calls(crlmmResultSet)["SNP_A-4208858",],

+plot(ex~calls(crlmmResult)["SNP_A-4208858",],

      xlab="Genotype Call for SNP_A-4208858",

      ylab="Expression", xaxt="n")

 axis(1, at=1:3, labels=c("AA", "AB", "BB"))

 @

+\section{Session Info}

+

+This vignette was created using the following packages:

 <<lksess>>=

 sessionInfo()

 @

Binary files a/inst/scripts/crlmmDownstream.pdf and b/inst/scripts/crlmmDownstream.pdf differ