[Genabel-commits] r1085 - in pkg/GenABEL: . R inst/unitTests man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 9 20:39:12 CET 2013
Author: yurii
Date: 2013-01-09 20:39:11 +0100 (Wed, 09 Jan 2013)
New Revision: 1085
Modified:
pkg/GenABEL/CHANGES.LOG
pkg/GenABEL/DESCRIPTION
pkg/GenABEL/R/GC.R
pkg/GenABEL/R/GC_ovdom.R
pkg/GenABEL/R/GenABEL.R
pkg/GenABEL/R/PGC.R
pkg/GenABEL/R/ccfast.R
pkg/GenABEL/R/ccfast.new.R
pkg/GenABEL/R/check.trait.R
pkg/GenABEL/R/egscore.R
pkg/GenABEL/R/egscore.old.R
pkg/GenABEL/R/formetascore.R
pkg/GenABEL/R/grammar.R
pkg/GenABEL/R/load.gwaa.data.R
pkg/GenABEL/R/polygenic.R
pkg/GenABEL/R/qtscore.R
pkg/GenABEL/R/rntransform.R
pkg/GenABEL/R/scan.haplo.2D.R
pkg/GenABEL/R/scan.haplo.R
pkg/GenABEL/R/ztransform.R
pkg/GenABEL/R/zzz.R
pkg/GenABEL/inst/unitTests/report.html
pkg/GenABEL/inst/unitTests/report.txt
pkg/GenABEL/inst/unitTests/reportSummary.txt
pkg/GenABEL/man/GC.Rd
pkg/GenABEL/man/GC_ovdom.Rd
pkg/GenABEL/man/GenABEL.Rd
pkg/GenABEL/man/PGC.Rd
pkg/GenABEL/man/Xfix.Rd
pkg/GenABEL/man/check.marker.Rd
pkg/GenABEL/man/grammar.Rd
pkg/GenABEL/man/srdta.Rd
pkg/GenABEL/man/ztransform.Rd
Log:
multiple changes related to changes in R and CRAN html layout
Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/CHANGES.LOG 2013-01-09 19:39:11 UTC (rev 1085)
@@ -1,5 +1,10 @@
-*** v. 1.7-3 (2013.01.07)
+*** v. 1.7-3 (2013.01.09)
+(2013.01.09)
+Commented the parts related to non-additive GC in qtscore
+Removed calls to 'attach' from multiple procedures
+Decrease of running time for long-running examples (GC_ovdom,GC,check.marker,Xfix,srdta)
+
(2013.01.07)
Fixing the problem which prevents the package from loading while checking the version on CRAN
Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/DESCRIPTION 2013-01-09 19:39:11 UTC (rev 1085)
@@ -2,7 +2,7 @@
Type: Package
Title: genome-wide SNP association analysis
Version: 1.7-3
-Date: 2013-01-07
+Date: 2013-01-09
Author: GenABEL project developers
Contact: GenABEL project developers <genabel.project at gmail.com>
Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru>
Modified: pkg/GenABEL/R/GC.R
===================================================================
--- pkg/GenABEL/R/GC.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/GC.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -33,11 +33,13 @@
#'
#' @examples
#' data(ge03d2)
-#' qts=mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "dominant")
-#' chi2.1df=results(qts)$chi2.1df
-#' s=summary(ge03d2)
-#' freq=s$Q.2
-#' result=GC(p=freq,x=1,method = "median",CA=FALSE,data=chi2.1df,n=nids(ge03d2))
+#' # truncate the data to make the example faster
+#' ge03d2 <- ge03d2[seq(from=1,to=nids(ge03d2),by=2),seq(from=1,to=nsnps(ge03d2),by=3)]
+#' qts <- mlreg(dm2~sex,data=ge03d2,gtmode = "dominant")
+#' chi2.1df <- results(qts)$chi2.1df
+#' s <- summary(ge03d2)
+#' freq <- s$Q.2
+#' result <- GC(p=freq,x=1,method = "median",CA=FALSE,data=chi2.1df,n=nids(ge03d2))
#'
#' @keywords htest
#'
Modified: pkg/GenABEL/R/GC_ovdom.R
===================================================================
--- pkg/GenABEL/R/GC_ovdom.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/GC_ovdom.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -30,11 +30,13 @@
#'
#' @examples
#' data(ge03d2)
-#' qts=mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "overdominant")
-#' chi2.1df=results(qts)$chi2.1df
-#' s=summary(ge03d2)
-#' freq=s$Q.2
-#' result=GC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))
+#' # truncate the data to make the example faster
+#' ge03d2 <- ge03d2[seq(from=1,to=nids(ge03d2),by=2),seq(from=1,to=nsnps(ge03d2),by=3)]
+#' qts <- mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "overdominant")
+#' chi2.1df <- results(qts)$chi2.1df
+#' s <- summary(ge03d2)
+#' freq <- s$Q.2
+#' result <- GC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))
#'
#' @keywords htest
#'
Modified: pkg/GenABEL/R/GenABEL.R
===================================================================
--- pkg/GenABEL/R/GenABEL.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/GenABEL.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -158,15 +158,25 @@
#' 46, 399-413.
#'
#' If you used environmental residuals from \code{\link{polygenic}} for
-#' \code{\link{qtscore}}, used GRAMMAR and/or GRAMMAS analysis, please cite
+#' \code{\link{qtscore}}, or used \code{\link{grammar}}, please cite
#'
+#' for original GRAMMAR
+#'
#' Aulchenko YS, de Koning DJ, Haley C. Genomewide rapid association using mixed model
#' and regression: a fast and simple method for genome-wide pedigree-based quantitative
#' trait loci association analysis. Genetics. 2007 177(1):577-85.
#'
+#' for GRAMMAR-GC
+#'
#' Amin N, van Duijn CM, Aulchenko YS. A genomic background based method for
-#' association analysis in related individuals. PLoS ONE. 2007 Dec 5;2(12):e1274.
+#' association analysis in related individuals. PLoS ONE. 2007 Dec 5;2(12):e1274.
#'
+#' for GRAMMAR-Gamma
+#'
+#' Svischeva G, Axenovich TI, Belonogova NM, van Duijn CM, Aulchenko YS. Rapid
+#' variance components-based method for whole-genome association analysis.
+#' Nature Genetics. 2012 44:1166-1170. doi:10.1038/ng.2410
+#'
#' If you used \code{\link{mmscore}}, please cite
#'
#' Chen WM, Abecasis GR. Family-based association tests for genome-wide association
Modified: pkg/GenABEL/R/PGC.R
===================================================================
--- pkg/GenABEL/R/PGC.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/PGC.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -27,7 +27,7 @@
#'
#' @examples
#' data(ge03d2)
-#' qts=qtscore(phdata(ge03d2)$dm2, ge03d2)
+#' qts=qtscore(dm2, ge03d2)
#' chi2.1df=results(qts)$chi2.1df
#' s=summary(ge03d2)
#' MAF=s$Q.2
Modified: pkg/GenABEL/R/ccfast.R
===================================================================
--- pkg/GenABEL/R/ccfast.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/ccfast.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -8,9 +8,10 @@
if (!quiet) cat("X-chromosome data dropped\n")
}
- attach(data at phdata,warn.conflicts=FALSE,pos=2)
- cc <- get(y,pos=2)
- detach(data at phdata)
+# attach(data at phdata,warn.conflicts=FALSE,pos=2)
+# cc <- get(y,pos=2)
+# detach(data at phdata)
+ cc <- phdata(data)[[y]]
if (length(levels(as.factor(cc)))<2) stop("cc status is monomorphic!")
if (length(levels(as.factor(cc)))>2) stop("cc status has more then 2 levels!")
Modified: pkg/GenABEL/R/ccfast.new.R
===================================================================
--- pkg/GenABEL/R/ccfast.new.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/ccfast.new.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -8,9 +8,10 @@
if (!quiet) cat("X-chromosome data dropped\n")
}
- attach(data at phdata,warn.conflicts=FALSE,pos=2)
- cc <- get(y,pos=2)
- detach(data at phdata)
+# attach(data at phdata,warn.conflicts=FALSE,pos=2)
+# cc <- get(y,pos=2)
+# detach(data at phdata)
+ cc <- phdata(data)[[y]]
if (length(levels(as.factor(cc)))<2) stop("cc status is monomorphic!")
if (length(levels(as.factor(cc)))>2) stop("cc status has more then 2 levels!")
Modified: pkg/GenABEL/R/check.trait.R
===================================================================
--- pkg/GenABEL/R/check.trait.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/check.trait.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -3,7 +3,8 @@
if (!is.data.frame(data)) {
if (is(data,"gwaa.data")) data <- data at phdata else stop("data should be a data frame or gwaa.data")
}
- attach(data,warn.conflicts=FALSE)
+# attach(data,warn.conflicts=FALSE)
+ with(data, {
rmvec <- rep(TRUE,length(trait))
for (i in 1:length(trait))
if (!is.numeric(get(trait[i]))) {
@@ -70,6 +71,7 @@
}
par(spar)
}
- detach(data)
+ })
+# detach(data)
}
Modified: pkg/GenABEL/R/egscore.R
===================================================================
--- pkg/GenABEL/R/egscore.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/egscore.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -13,7 +13,11 @@
if (length(strata)!=data at gtdata@nids) stop("Strata variable and the data do not match in length")
if (any(is.na(strata))) stop("Strata variable contains NAs")
- if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
+ if ( is(try(formula,silent=TRUE),"try-error") ) {
+ formula <- phdata(data)[[as(match.call()[["formula"]],"character")]]
+ }
+
+# if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
if (is(formula,"formula")) {
mf <- model.frame(formula,data,na.action=na.omit,drop.unused.levels=TRUE)
y <- model.response(mf)
@@ -30,7 +34,7 @@
} else {
stop("formula argument must be a formula or one of (numeric, integer, double)")
}
- if (!missing(data)) detach(data at phdata)
+# if (!missing(data)) detach(data at phdata)
if (length(strata)!=data at gtdata@nids) stop("Strata variable and the data do not match in length")
if (any(is.na(strata))) stop("Strata variable contains NAs")
if (any(strata!=0)) {
Modified: pkg/GenABEL/R/egscore.old.R
===================================================================
--- pkg/GenABEL/R/egscore.old.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/egscore.old.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -12,7 +12,11 @@
if (length(strata)!=data at gtdata@nids) stop("Strata variable and the data do not match in length")
if (any(is.na(strata))) stop("Strata variable contains NAs")
- if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
+ if ( is(try(formula,silent=TRUE),"try-error") ) {
+ formula <- phdata(data)[[as(match.call()[["formula"]],"character")]]
+ }
+
+# if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
if (is(formula,"formula")) {
mf <- model.frame(formula,data,na.action=na.omit,drop.unused.levels=TRUE)
y <- model.response(mf)
@@ -29,7 +33,7 @@
} else {
stop("formula argument must be a formula or one of (numeric, integer, double)")
}
- if (!missing(data)) detach(data at phdata)
+# if (!missing(data)) detach(data at phdata)
if (length(strata)!=data at gtdata@nids) stop("Strata variable and the data do not match in length")
if (any(is.na(strata))) stop("Strata variable contains NAs")
if (any(strata!=0)) {
Modified: pkg/GenABEL/R/formetascore.R
===================================================================
--- pkg/GenABEL/R/formetascore.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/formetascore.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -2,7 +2,12 @@
function(formula,data,stat=qtscore,transform="no",build="unknown",verbosity=1, ...) {
if (!is(data,"gwaa.data")) stop("data argument must have gwaa.data-class")
checkphengen(data)
- if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
+
+ if ( is(try(formula,silent=TRUE),"try-error") ) {
+ formula <- phdata(data)[[as(match.call()[["formula"]],"character")]]
+ }
+
+ # if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
if (is(formula,"polygenic")) {
pm <- pmatch("stat",names(match.call()))
pm <- (pm[!is.na(pm)])[1]
@@ -24,7 +29,7 @@
} else {
mids <- which(!is.na(formula))
}
- if (!missing(data)) detach(data at phdata)
+# if (!missing(data)) detach(data at phdata)
if (verbosity<0) stop("verbosity parameter must be positive integer")
res <- stat(formula,data,...)
sum <- summary(data at gtdata[mids,])
Modified: pkg/GenABEL/R/grammar.R
===================================================================
--- pkg/GenABEL/R/grammar.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/grammar.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -33,18 +33,21 @@
#'
#' @references
#'
-#' GRAMMAR-Raw: Aulchenko YS, de Koning DJ, Haley C.
+#' GRAMMAR-Raw:
+#' Aulchenko YS, de Koning DJ, Haley C.
#' Genomewide rapid association using mixed model and regression: a fast and
#' simple method for genomewide pedigree-based quantitative trait loci
#' association analysis. Genetics. 2007 Sep;177(1):577-85.
#'
-#' GRAMMAR-GC: Amin N, van Duijn CM, Aulchenko YS.
+#' GRAMMAR-GC:
+#' Amin N, van Duijn CM, Aulchenko YS.
#' A genomic background based method for association analysis in related individuals.
#' PLoS One. 2007 Dec 5;2(12):e1274.
#'
-#' GRAMMAR-Gamma: Svisheva GR, Axenovich TI, Belonogova MN, van Duijn CM, Aulchenko YS.
-#' Rapid variance componentsÐbased method for whole-genome association analysis.
-#' Nature Genetics. 2012 (http://dx.doi.org/10.1038/ng.2410)
+#' GRAMMAR-Gamma:
+#' Svischeva G, Axenovich TI, Belonogova NM, van Duijn CM, Aulchenko YS.
+#' Rapid variance components-based method for whole-genome association analysis.
+#' Nature Genetics. 2012 44:1166-1170. doi:10.1038/ng.2410
#'
#' @examples
#' # Using clean ge03d2 data
Modified: pkg/GenABEL/R/load.gwaa.data.R
===================================================================
--- pkg/GenABEL/R/load.gwaa.data.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/load.gwaa.data.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -12,7 +12,7 @@
stop("the column named \"sex\", containing the male identifier was not found in the phenofile")
#### 2.8.0!
v <- version
- if ((as.numeric(v$major) >= 2) && (as.numeric(v$minor) >= 8.0)) {
+ if ( as.numeric(v$major) > 2 || ((as.numeric(v$major) == 2) && (as.numeric(v$minor) >= 8.0)) ) {
a <- table(dta$sex,useNA="ifany")
} else {
a <- table(dta$sex,exclude=NULL)
Modified: pkg/GenABEL/R/polygenic.R
===================================================================
--- pkg/GenABEL/R/polygenic.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/polygenic.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -201,8 +201,12 @@
else if (llfun == "polylik") llFUN <- polylik
else stop("llfun should be 'polylik' or 'polylik_eigen'")
- if (!missing(data)) attach(data,pos=2,warn.conflicts=FALSE)
+ if ( is(try(formula,silent=TRUE),"try-error") ) {
+ formula <- data[[as(match.call()[["formula"]],"character")]]
+ }
+# if (!missing(data)) attach(data,pos=2,warn.conflicts=FALSE)
+
# beging patch bug #1322 (by Nicola Pirastu)
if (is(formula, "formula")){
mf <- model.frame(formula, data, na.action = na.omit,
@@ -281,7 +285,7 @@
}
}
- if (!missing(data)) detach(data)
+# if (!missing(data)) detach(data)
tmp <- t(relmat)
relmat[upper.tri(relmat)] <- tmp[upper.tri(tmp)]
rm(tmp);gc()
Modified: pkg/GenABEL/R/qtscore.R
===================================================================
--- pkg/GenABEL/R/qtscore.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/qtscore.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -102,8 +102,13 @@
out <- paste("trait.type argument should be one of",ttargs,"\n")
stop(out)
}
+
+ if ( is(try(formula,silent=TRUE),"try-error") ) {
+ formula <- phdata(data)[[as(match.call()[["formula"]],"character")]]
+ }
+
if (trait.type=="guess") {
- if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
+# if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
if (is(formula,"formula")) {
mf <- model.frame(formula,data,na.action=na.omit,drop.unused.levels=TRUE)
y <- model.response(mf)
@@ -115,12 +120,12 @@
stop("formula argument must be a formula or one of (numeric, integer, double)")
}
warning(paste("trait type is guessed as",trait.type))
- if (!missing(data)) detach(data at phdata)
+# if (!missing(data)) detach(data at phdata)
}
if (trait.type=="gaussian") fam <- gaussian()
if (trait.type=="binomial") fam <- binomial()
- if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
+# if (!missing(data)) attach(data at phdata,pos=2,warn.conflicts=FALSE)
if (is(formula,"formula")) {
mf <- model.frame(formula,data,na.action=na.omit,drop.unused.levels=TRUE)
y <- model.response(mf)
@@ -146,7 +151,7 @@
} else {
stop("formula argument should be a formula or a numeric vector")
}
- if (!missing(data)) detach(data at phdata)
+# if (!missing(data)) detach(data at phdata)
if (length(strata)!=nids(data)) stop("Strata variable and the data do not match in length")
if (any(is.na(strata))) stop("Strata variable contains NAs")
if (any(strata!=0)) {
@@ -235,16 +240,16 @@
actdf[abs(actdf+999.99)<1.e-8] <- 1.e-16 #NA
# out$actdf <- actdf
###out$chi2.2df <- chi2.2df
- z0 <- chi2[(7*lenn+1):(8*lenn)];
- z0[abs(z0+999.99)<1.e-8] <- 0 #NA
-# out$z0 <- z0
- z2 <- chi2[(8*lenn+1):(9*lenn)];
- z2[abs(z2+999.99)<1.e-8] <- 0 #NA
-# out$z2 <- z2
- rho <- chi2[(9*lenn+1):(10*lenn)];
- rho[abs(rho+999.99)<1.e-8] <- 0 #NA
-# rho <- abs(rho)
-# out$rho <- rho
+# z0 <- chi2[(7*lenn+1):(8*lenn)];
+# z0[abs(z0+999.99)<1.e-8] <- 0 #NA
+## out$z0 <- z0
+# z2 <- chi2[(8*lenn+1):(9*lenn)];
+# z2[abs(z2+999.99)<1.e-8] <- 0 #NA
+## out$z2 <- z2
+# rho <- chi2[(9*lenn+1):(10*lenn)];
+# rho[abs(rho+999.99)<1.e-8] <- 0 #NA
+## rho <- abs(rho)
+## out$rho <- rho
lambda <- list()
if (is.logical(clambda)) {
@@ -276,21 +281,21 @@
}
chi2.c1df <- chi2.1df/lambda$estimate
- if (is.logical(clambda)) {
- lambda$iz0 <- estlambda(z0*z0,plot=FALSE,proportion=propPs)$estimate
- lambda$iz2 <- estlambda(z2*z2,plot=FALSE,proportion=propPs)$estimate
- if (clambda && lambda$iz0<1.0) {warning("z0 lambda < 1, set to 1");lambda$iz0<-1.0}
- if (clambda && lambda$iz2<1.0) {warning("z2 lambda < 1, set to 1");lambda$iz2<-1.0}
- chi2.c2df <- (z0*z0/lambda$iz0 + z2*z2/lambda$iz2 - 2.*z0*z2*rho/(sqrt(lambda$iz0*lambda$iz2)))/(1.- rho*rho)
- } else {
- if (is.list(clambda) && !any(is.na(match(c("estimate","iz0","iz2"),names(clambda))))) {
- chi2.c2df <- (z0*z0/lambda$iz0 + z2*z2/lambda$iz2 - 2.*z0*z2*rho/(sqrt(lambda$iz0*lambda$iz2)))/(1.- rho*rho)
- } else {
- lambda$iz0 <- 1.0
- lambda$iz2 <- 1.0
- chi2.c2df <- chi2.2df
- }
- }
+# if (is.logical(clambda)) {
+# lambda$iz0 <- estlambda(z0*z0,plot=FALSE,proportion=propPs)$estimate
+# lambda$iz2 <- estlambda(z2*z2,plot=FALSE,proportion=propPs)$estimate
+# if (clambda && lambda$iz0<1.0) {warning("z0 lambda < 1, set to 1");lambda$iz0<-1.0}
+# if (clambda && lambda$iz2<1.0) {warning("z2 lambda < 1, set to 1");lambda$iz2<-1.0}
+# chi2.c2df <- (z0*z0/lambda$iz0 + z2*z2/lambda$iz2 - 2.*z0*z2*rho/(sqrt(lambda$iz0*lambda$iz2)))/(1.- rho*rho)
+# } else {
+# if (is.list(clambda) && !any(is.na(match(c("estimate","iz0","iz2"),names(clambda))))) {
+# chi2.c2df <- (z0*z0/lambda$iz0 + z2*z2/lambda$iz2 - 2.*z0*z2*rho/(sqrt(lambda$iz0*lambda$iz2)))/(1.- rho*rho)
+# } else {
+# lambda$iz0 <- 1.0
+# lambda$iz2 <- 1.0
+# chi2.c2df <- chi2.2df
+# }
+# }
effB <- chi2[(3*lenn+1):(lenn*4)]
effB[abs(effB+999.99)<1.e-8] <- NA
effAB <- chi2[(4*lenn+1):(lenn*5)]
@@ -308,7 +313,7 @@
pr.1df <- pr.1df + 1*(chi2.1df < th1)
pr.2df <- pr.2df + 1*(chi2.2df < max(chi2[(lenn+1):(2*lenn)]))
pr.c1df <- pr.c1df + 1*(chi2.c1df < th1)
- pr.c2df <- pr.c2df + 1*(chi2.c2df < th1)
+# pr.c2df <- pr.c2df + 1*(chi2.c2df < th1)
# if (!quiet && ((j-1)/bcast == round((j-1)/bcast))) {
## cat("\b\b\b\b\b\b",round((100*(j-1)/times),digits=2),"%",sep="")
# cat(" ",round((100*(j-1)/times),digits=2),"%",sep="")
Modified: pkg/GenABEL/R/rntransform.R
===================================================================
--- pkg/GenABEL/R/rntransform.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/rntransform.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -1,5 +1,13 @@
"rntransform" <-
-function(formula,data,family=gaussian) {
+ function(formula,data,family=gaussian) {
+
+ if ( is(try(formula,silent=TRUE),"try-error") ) {
+ if ( is(data,"gwaa.data") ) data1 <- phdata(data)
+ else if ( is(data,"data.frame") ) data1 <- data
+ else stop("'data' must have 'gwaa.data' or 'data.frame' class")
+ formula <- data1[[as(match.call()[["formula"]],"character")]]
+ }
+
var <- ztransform(formula,data,family)
out <- rank(var) - 0.5
out[is.na(var)] <- NA
Modified: pkg/GenABEL/R/scan.haplo.2D.R
===================================================================
--- pkg/GenABEL/R/scan.haplo.2D.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/scan.haplo.2D.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -11,20 +11,20 @@
avrs <- all.vars(as.formula(formula))
if (!any(avrs=="CRSNP")) stop("formula must contain CRSNP variable to be replaced with the analysis SNPs")
avrs <- avrs[avrs!="CRSNP"]
- attach(data at phdata,pos=2,warn.conflicts=FALSE)
+ #attach(data at phdata,pos=2,warn.conflicts=FALSE)
cov <- NA
if (length(avrs)>1) {
- cov <- matrix(get(avrs[2],pos=2),ncol=1)
- if (length(avrs>2)) for (i in 3:length(avrs)) cov <- cbind(cov,get(avrs[i],pos=2))
+ cov <- matrix(phdata(data)[[avrs[2]]],ncol=1)
+ if (length(avrs>2)) for (i in 3:length(avrs)) cov <- cbind(cov,phdata(data)[[avrs[i]]])
}
- tra <- get(avrs[1],pos=2)
+ tra <- phdata(data)[[avrs[1]]]
if (missing(trait.type)) {
if (length(unique(tra))==2)
trait.type<-"binomial"
else
trait.type<-"gaussian"
}
- detach(data at phdata)
+ #detach(data at phdata)
if (length(unique(tra))<2) stop("Trait is monomorphic!")
Modified: pkg/GenABEL/R/scan.haplo.R
===================================================================
--- pkg/GenABEL/R/scan.haplo.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/scan.haplo.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -11,20 +11,20 @@
avrs <- all.vars(as.formula(formula))
if (!any(avrs=="CRSNP")) stop("formula must contain CRSNP variable to be replaced with the analysis SNPs")
avrs <- avrs[avrs!="CRSNP"]
- attach(data at phdata,pos=2,warn.conflicts=FALSE)
+# attach(data at phdata,pos=2,warn.conflicts=FALSE)
cov <- NA
if (length(avrs)>1) {
- cov <- get(avrs[2],pos=2)
- if (length(avrs)>2) for (i in 3:length(avrs)) cov <- cbind(cov,get(avrs[i],pos=2))
+ cov <- phdata(data)[[avrs[2]]]
+ if (length(avrs)>2) for (i in 3:length(avrs)) cov <- cbind(cov,phdata(data)[[avrs[i]]])
}
- tra <- get(avrs[1],pos=2)
+ tra <- phdata(data)[[avrs[1]]]
if (missing(trait.type)) {
if (length(unique(tra))==2)
trait.type<-"binomial"
else
trait.type<-"gaussian"
}
- detach(data at phdata)
+# detach(data at phdata)
if (length(unique(tra))<2) stop("Trait is monomorphic!")
Modified: pkg/GenABEL/R/ztransform.R
===================================================================
--- pkg/GenABEL/R/ztransform.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/ztransform.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -5,7 +5,7 @@
data <- environment(formula)
else
data <- environment()
- wasdata <- 0
+# wasdata <- 0
} else {
if (is(data,"gwaa.data")) {
data <- data at phdata
@@ -13,8 +13,8 @@
else if (!is(data,"data.frame")) {
stop("data argument should be of gwaa.data or data.frame class")
}
- attach(data,pos=2,warn.conflicts=FALSE)
- wasdata <- 1
+# attach(data,pos=2,warn.conflicts=FALSE)
+# wasdata <- 1
}
if (is.character(family))
@@ -25,15 +25,20 @@
print(family)
stop("'family' not recognized")
}
+
+ if ( is(try(formula,silent=TRUE),"try-error") ) {
+ formula <- data[[as(match.call()[["formula"]],"character")]]
+ }
+
if (is(formula,"formula")) {
mf <- model.frame(formula,data,na.action=na.omit,drop.unused.levels=TRUE)
y <- model.response(mf)
desmat <- model.matrix(formula,mf)
lmf <- glm.fit(desmat,y,family=family)
- if (wasdata)
- mids <- rownames(data) %in% rownames(mf)
- else
- mids <- (!is.na(get(as.character(formula[2]))))
+# if (wasdata)
+# mids <- rownames(data) %in% rownames(mf)
+# else
+ mids <- complete.cases(desmat,y)
resid <- lmf$resid
# print(formula)
} else if (is(formula,"numeric") || is(formula,"integer") || is(formula,"double")) {
@@ -47,7 +52,7 @@
stop("formula argument must be a formula or one of (numeric, integer, double)")
}
y <- (resid-mean(resid))/sd(resid)
- if (wasdata==1) detach(data)
+# if (wasdata==1) detach(data)
tmeas <- as.logical(mids)
out <- rep(NA,length(mids))
out[tmeas] <- y
Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/R/zzz.R 2013-01-09 19:39:11 UTC (rev 1085)
@@ -1,11 +1,11 @@
-.onLoad <- function(lib, pkg) {
+.onAttach <- function(lib, pkg) {
## this is something which should be fixed: both version
## and date can come from DESCRIPTION!
#pkgDescription <- packageDescription(pkg)
#pkgVersion <- pkgDescription$Version
#pkgDate <- pkgDescription$Date
pkgVersion <- "1.7-3"
- pkgDate <- "January 07, 2013"
+ pkgDate <- "January 09, 2013"
welcomeMessage <- paste(pkg," v. ",pkgVersion," (",pkgDate,") loaded\n",sep="")
# check if CRAN version is the same as loaded
cranVersion <- try( checkPackageVersionOnCRAN(pkg) )
Modified: pkg/GenABEL/inst/unitTests/report.html
===================================================================
--- pkg/GenABEL/inst/unitTests/report.html 2013-01-08 20:54:14 UTC (rev 1084)
+++ pkg/GenABEL/inst/unitTests/report.html 2013-01-09 19:39:11 UTC (rev 1085)
@@ -1,8 +1,8 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/transitional.dtd">
-<html><head><title>RUNIT TEST PROTOCOL--Mon Dec 3 21:50:27 2012</title>
+<html><head><title>RUNIT TEST PROTOCOL--Wed Jan 9 20:36:47 2013</title>
</head>
-<body><h1 TRUE>RUNIT TEST PROTOCOL--Mon Dec 3 21:50:27 2012</h1>
+<body><h1 TRUE>RUNIT TEST PROTOCOL--Wed Jan 9 20:36:47 2013</h1>
<p>Number of test functions: 18</p>
<p style=color:red>Number of errors: 1</p>
<p>Number of failures: 0</p>
@@ -35,9 +35,9 @@
<hr>
<h3 TRUE>Details</h3>
<p><a name="GenABEL unit testing"><h5 TRUE>Test Suite: GenABEL unit testing</h5>
-</a>Test function regexp: ^test.+<br/>Test file regexp: ^runit.+\.[rR]$<br/>Involved directory:<br/>/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests<br/><ul><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R">Test file: runit.convert.snp.ped.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.ped.R_test.convert.snp.ped">test.convert.snp.ped: (0 checks) ... OK (0.03 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R">Test file: runit.convert.snp.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.R_test.convert.snp">test.convert.snp: (4 checks) ... OK (1.08 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R">Test file: runit.descriptives.trait.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.descriptives.trait.R_test.descriptives.trait">test.descriptives.trait: (1 checks) ... OK (0.49 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R">Test file: runit.exports.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.exports.R_test.exports">test.exports: (19 checks) ... OK (0.62 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R">Test file: runit.findRelatives.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.findRelatives.R_test.findRelatives">test.findRelatives: (10 checks) ... OK (54.73 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx_large.R">Test file: runit.impute2xxx_large.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx_large.R_test.impute2xxx_large">test.impute2xxx_large: (0 checks) ... OK (0 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R">Test file: runit.impute2xxx.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx.R_test.impute2databel"><u style=color:red>test.impute2databel: ERROR !! </u></a>Error in .Call("iterator", tmp_fv at data, as.integer(0), as.integer(0), :
+</a>Test function regexp: ^test.+<br/>Test file regexp: ^runit.+\.[rR]$<br/>Involved directory:<br/>/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests<br/><ul><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R">Test file: runit.convert.snp.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.R_test.convert.snp">test.convert.snp: (4 checks) ... OK (1.02 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R">Test file: runit.convert.snp.ped.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.ped.R_test.convert.snp.ped">test.convert.snp.ped: (0 checks) ... OK (0.03 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R">Test file: runit.descriptives.trait.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.descriptives.trait.R_test.descriptives.trait">test.descriptives.trait: (1 checks) ... OK (0.43 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R">Test file: runit.exports.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.exports.R_test.exports">test.exports: (15 checks) ... OK (0.5 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R">Test file: runit.findRelatives.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.findRelatives.R_test.findRelatives">test.findRelatives: (10 checks) ... OK (46.07 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R">Test file: runit.impute2xxx.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx.R_test.impute2databel"><u style=color:red>test.impute2databel: ERROR !! </u></a>Error in .Call("iterator", tmp_fv at data, as.integer(0), as.integer(0), :
"iterator" not resolved from current namespace (GenABEL)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1085
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