git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38586 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -137,3 +137,9 @@ is decoded and scanned |
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2009-04-08 Matt Ritchie - committed version 1.0.79 |
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* fixed bug in readIDAT and readIdatFiles from reading in RunInfo header information |
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+ |
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+2009-04-07 B Carvalho - committed version 1.0.80 (advantages of being a lot of hours behind) |
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+ |
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+* Fixed downstream vignette to account for the SnpSet object being returned by crlmm |
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+ |
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+* Fixed some minor status messages |
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@@ -1,7 +1,7 @@ |
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Package: crlmm |
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Type: Package |
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-Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays. |
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-Version: 1.0.79 |
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+Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
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+Version: 1.0.80 |
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Date: 2008-12-30 |
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Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
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Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
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@@ -100,7 +100,7 @@ crlmmGT <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL, |
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keepIndex[which(gender[keepIndex]==2)], |
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keepIndex[which(gender[keepIndex]==1)]) |
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- if(verbose) cat("Calling", NR, "SNPs for recalibration") |
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+ if(verbose) cat("Calling", NR, "SNPs for recalibration... ") |
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|
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## call C |
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fIndex <- which(gender==2) |
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@@ -185,7 +185,7 @@ crlmmGT <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL, |
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params[-2] <- newparams[-2] |
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|
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rm(newparams);gc(verbose=FALSE) |
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- if(verbose) cat("Calling", NR, "SNPs") |
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+ if(verbose) cat("Calling", NR, "SNPs... ") |
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## ################### |
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## ## MOVE TO C####### |
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ImNull <- gtypeCallerR2(A, B, fIndex, mIndex, params[["centers"]], |
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@@ -426,7 +426,7 @@ crlmmGTTNoN <- function(A, B, SNR, mixtureParams, cdfName, |
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keepIndex[which(gender[keepIndex]==2)], |
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keepIndex[which(gender[keepIndex]==1)]) |
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- if(verbose) cat("Calling", NR, "SNPs for recalibration") |
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+ if(verbose) cat("Calling", NR, "SNPs for recalibration... ") |
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## call C |
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fIndex <- which(gender==2) |
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@@ -498,7 +498,7 @@ crlmmGTTNoN <- function(A, B, SNR, mixtureParams, cdfName, |
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## BC: must keep SD |
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params[-2] <- newparams[-2] |
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rm(newparams);gc(verbose=FALSE) |
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- if(verbose) cat("Calling", NR, "SNPs") |
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+ if(verbose) cat("Calling", NR, "SNPs... ") |
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## ################### |
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## ## MOVE TO C####### |
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t0 <- proc.time() |
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@@ -592,7 +592,7 @@ crlmmGTNormalNoN <- function(A, B, SNR, mixtureParams, cdfName, |
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keepIndex[which(gender[keepIndex]==2)], |
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keepIndex[which(gender[keepIndex]==1)]) |
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- if(verbose) cat("Calling", NR, "SNPs for recalibration") |
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+ if(verbose) cat("Calling", NR, "SNPs for recalibration... ") |
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## call C |
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fIndex <- which(gender==2) |
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@@ -664,7 +664,7 @@ crlmmGTNormalNoN <- function(A, B, SNR, mixtureParams, cdfName, |
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## BC: must keep SD |
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params[-2] <- newparams[-2] |
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rm(newparams);gc(verbose=FALSE) |
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- if(verbose) cat("Calling", NR, "SNPs") |
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+ if(verbose) cat("Calling", NR, "SNPs... ") |
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## ################### |
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## ## MOVE TO C####### |
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t0 <- proc.time() |
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@@ -773,7 +773,7 @@ crlmmGTnm <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL, |
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keepIndex[which(gender[keepIndex]==2)], |
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keepIndex[which(gender[keepIndex]==1)]) |
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- if(verbose) cat("Calling", NR, "SNPs for recalibration") |
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+ if(verbose) cat("Calling", NR, "SNPs for recalibration... ") |
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## call C |
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fIndex <- which(gender==2) |
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@@ -858,7 +858,7 @@ crlmmGTnm <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL, |
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params[-2] <- newparams[-2] |
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rm(newparams);gc(verbose=FALSE) |
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- if(verbose) cat("Calling", NR, "SNPs") |
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+ if(verbose) cat("Calling", NR, "SNPs... ") |
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## ################### |
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## ## MOVE TO C####### |
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t0 <- proc.time() |
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@@ -57,14 +57,12 @@ if (!exists("crlmmResult")) { |
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} |
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@ |
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-This is currently a list. |
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+This is currently a \Rclass{SnpSet} object. |
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<<lkj21>>= |
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class(crlmmResult) |
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- sapply(crlmmResult, dim) |
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- sapply(crlmmResult, length) |
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@ |
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-\section{Constructing an eSet extension} |
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+\section{Adding information to a \Rclass{SnpSet}} |
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We will use the \Rpackage{GGdata} package to obtain extra information |
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on the samples. This will be later used when building an \Rclass{eSet} |
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@@ -74,30 +72,27 @@ extension to store the genotyping results. |
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if (!exists("hmceuB36")) data(hmceuB36) |
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pd <- phenoData(hmceuB36) |
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ggn <- sampleNames(pd) |
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- preSN <- colnames(crlmmResult[["calls"]]) |
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+ preSN <- sampleNames(crlmmResult) |
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simpSN <- gsub("_.*", "", preSN) |
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if (!all.equal(simpSN, ggn)) stop("align GGdata phenoData with crlmmResult read") |
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@ |
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-The list obtained as output of the \Rmethod{crlmm} method can be |
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-easily coerced to an eSet extension with the help of the helper |
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-function \Rfunction{list2crlmmSet}. |
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+The additional information obtained from \Rpackage{GGdata} can be |
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+easily combined to what is already available on \Robject{crlmmResult}. |
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<<docl>>= |
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- colnames(crlmmResult[["calls"]]) <- colnames(crlmmResult[["confs"]]) <- simpSN |
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- crlmmResultSet <- list2crlmmSet(crlmmResult) |
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- phenoData(crlmmResultSet) <- combine(pd, phenoData(crlmmResultSet)) |
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- crlmmResultSet |
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- dim(calls(crlmmResultSet)) |
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- dim(confs(crlmmResultSet)) |
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- calls(crlmmResultSet)[1:10, 1:2] |
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- confs(crlmmResultSet)[1:10, 1:2] |
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+ sampleNames(crlmmResult) <- simpSN |
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+ phenoData(crlmmResult) <- combine(pd, phenoData(crlmmResult)) |
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+ dim(calls(crlmmResult)) |
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+ dim(confs(crlmmResult)) |
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+ calls(crlmmResult)[1:10, 1:2] |
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+ confs(crlmmResult)[1:10, 1:2] |
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@ |
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\section{Coercing to snp.matrix as a prelude to a GWAS} |
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<<lksnm>>= |
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library(snpMatrix) |
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-crlmmSM <- as(t(calls(crlmmResultSet))-1, "snp.matrix") |
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+crlmmSM <- as(t(calls(crlmmResult))-1, "snp.matrix") |
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crlmmSM |
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@ |
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@@ -116,12 +111,15 @@ gwas <- snp.rhs.tests(ex~male, data=subjdata, snp.data=crlmmSM, family="gaussian |
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ok <- which(p.value(gwas) < 1e-10) |
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gwas[ok,] |
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<<dopl,fig=TRUE>>= |
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-plot(ex~calls(crlmmResultSet)["SNP_A-4208858",], |
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+plot(ex~calls(crlmmResult)["SNP_A-4208858",], |
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xlab="Genotype Call for SNP_A-4208858", |
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ylab="Expression", xaxt="n") |
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axis(1, at=1:3, labels=c("AA", "AB", "BB")) |
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@ |
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+\section{Session Info} |
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+ |
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+This vignette was created using the following packages: |
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<<lksess>>= |
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sessionInfo() |
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@ |