[Genabel-commits] r1218 - in pkg/GenABEL: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu May 16 14:41:41 CEST 2013
Author: yurii
Date: 2013-05-16 14:41:40 +0200 (Thu, 16 May 2013)
New Revision: 1218
Modified:
pkg/GenABEL/CHANGES.LOG
pkg/GenABEL/DESCRIPTION
pkg/GenABEL/R/hom.R
pkg/GenABEL/R/zzz.R
pkg/GenABEL/man/GenABEL.Rd
pkg/GenABEL/man/catable.Rd
pkg/GenABEL/man/ccfast.Rd
pkg/GenABEL/man/check.marker-class.Rd
pkg/GenABEL/man/check.marker.Rd
pkg/GenABEL/man/convert.snp.affymetrix.Rd
pkg/GenABEL/man/convert.snp.mach.Rd
pkg/GenABEL/man/egscore.old.Rd
pkg/GenABEL/man/emp.qtscore.Rd
pkg/GenABEL/man/export.merlin.Rd
pkg/GenABEL/man/hom.old.Rd
pkg/GenABEL/man/ibs.old.Rd
pkg/GenABEL/man/merge.snp.data.Rd
pkg/GenABEL/man/mmscore.Rd
pkg/GenABEL/man/npsubtreated.Rd
pkg/GenABEL/man/plot.check.marker.Rd
pkg/GenABEL/man/scan.haplo.2D.Rd
pkg/GenABEL/man/scan.haplo.Rd
pkg/GenABEL/man/snp.subset.Rd
pkg/GenABEL/man/srdta.Rd
Log:
Fixed too long lines in Rd files
Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/CHANGES.LOG 2013-05-16 12:41:40 UTC (rev 1218)
@@ -1,5 +1,8 @@
*** v. 1.7-6
+(2013.05.16)
+Fixed too long lines in Rd files.
+
(2013.05.15)
Updated version number to 1.7-6 (release), checked with latest
dev-version of R available. Added 'bigRR' as suggested package.
Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/DESCRIPTION 2013-05-16 12:41:40 UTC (rev 1218)
@@ -2,7 +2,7 @@
Type: Package
Title: genome-wide SNP association analysis
Version: 1.7-6
-Date: 2013-05-15
+Date: 2013-05-16
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/hom.R
===================================================================
--- pkg/GenABEL/R/hom.R 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/R/hom.R 2013-05-16 12:41:40 UTC (rev 1218)
@@ -72,7 +72,8 @@
#' h[1:5,]
#' homsem <- h[,"Hom"]*(1-h[,"Hom"])/h[,"NoMeasured"]
#' plot(h[,"Hom"],homsem)
-#' # wrong analysis: one should use all people (for right frequency) and markers (for right F) available!
+#' # wrong analysis: one should use all people (for right frequency)
+#' # and markers (for right F) available!
#' h <- hom(ge03d2[,c(1:10)])
#' h
#'
Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/R/zzz.R 2013-05-16 12:41:40 UTC (rev 1218)
@@ -5,7 +5,7 @@
#pkgVersion <- pkgDescription$Version
#pkgDate <- pkgDescription$Date
pkgVersion <- "1.7-6"
- pkgDate <- "May 15, 2013"
+ pkgDate <- "May 16, 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/man/GenABEL.Rd
===================================================================
--- pkg/GenABEL/man/GenABEL.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/GenABEL.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -1,8 +1,8 @@
\docType{package}
\name{GenABEL}
+\alias{genabel}
\alias{GenABEL}
\alias{GenABEL-package}
-\alias{genabel}
\title{GWAS in R}
\description{
GenABEL: an R package for Genome Wide Association
Modified: pkg/GenABEL/man/catable.Rd
===================================================================
--- pkg/GenABEL/man/catable.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/catable.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -6,7 +6,8 @@
which fall between user-defined categories
}
\usage{
-catable(data, categories = c(quantile(data,c(0.01,0.1,0.5,0.9,0.99),na.rm=TRUE)), cumulative = FALSE, na.rm = TRUE, digits = 3)
+catable(data, categories = c(quantile(data,c(0.01,0.1,0.5,0.9,0.99),na.rm=TRUE)),
+ cumulative = FALSE, na.rm = TRUE, digits = 3)
}
\arguments{
\item{data}{A vector of numerics}
Modified: pkg/GenABEL/man/ccfast.Rd
===================================================================
--- pkg/GenABEL/man/ccfast.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/ccfast.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -6,7 +6,8 @@
from 2x2 (allelic) or 2x3 (genotypic) tables
}
\usage{
-ccfast(y, data, snpsubset, idsubset, times=1, quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0)
+ccfast(y, data, snpsubset, idsubset, times=1, quiet=FALSE,bcast=10,
+ clambda=TRUE,propPs=1.0)
}
\arguments{
\item{y}{character name of the vector of case-control status. Cases are denoted as 1 and controls as 0.}
Modified: pkg/GenABEL/man/check.marker-class.Rd
===================================================================
--- pkg/GenABEL/man/check.marker-class.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/check.marker-class.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -18,7 +18,8 @@
\item{nofreq}{Markers with MAF < specified maf}
\item{Xmrkfail}{X-linked markers with too many heterozygous male genotypes}
\item{redundant}{Redundant markers}
-\item{details.redundancy}{List with details on redundant markers (reference-marker <-> redundant-markers)}
+\item{details.redundancy}{List with details on redundant markers (reference-marker
+ <-> redundant-markers)}
\item{idnocall}{People with too low SNP call rate across al SNPs}
\item{hetfail}{People having too high heterozygosity}
\item{ibsfail}{People having too high IBS with other people}
@@ -50,7 +51,8 @@
}
\examples{
data(srdta)
-mc <- check.marker(data=srdta at gtdata[,1:100],redundant="all",maf=0.01,minconcordance=0.9,fdr=.1,ibs.mrk=0)
+mc <- check.marker(data=srdta at gtdata[,1:100],redundant="all",maf=0.01,
+ minconcordance=0.9,fdr=.1,ibs.mrk=0)
class(mc)
names(mc)
names(mc$call)
Modified: pkg/GenABEL/man/check.marker.Rd
===================================================================
--- pkg/GenABEL/man/check.marker.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/check.marker.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -10,11 +10,11 @@
}
\usage{
check.marker(data, snpsubset, idsubset, callrate = 0.95,
- perid.call=0.95, extr.call = 0.1, extr.perid.call = 0.1, het.fdr = 0.01,
- ibs.threshold = 0.95, ibs.mrk = 2000, ibs.exclude="both", maf, p.level = -1, fdrate = 0.2,
- odds = 1000, hweidsubset, redundant = "no",
- minconcordance = 2.0, qoption = "bh95", imphetasmissing = TRUE, XXY.call=0.8,
- intermediateXF = c(0.5, 0.5))
+ perid.call=0.95, extr.call = 0.1, extr.perid.call = 0.1, het.fdr = 0.01,
+ ibs.threshold = 0.95, ibs.mrk = 2000, ibs.exclude="both", maf, p.level = -1,
+ fdrate = 0.2, odds = 1000, hweidsubset, redundant = "no",
+ minconcordance = 2.0, qoption = "bh95", imphetasmissing = TRUE, XXY.call=0.8,
+ intermediateXF = c(0.5, 0.5))
}
\arguments{
\item{data}{gwaa.data or snp.data object}
@@ -119,7 +119,8 @@
mc <- check.marker(data=srdta,ids=c(1:300),call=.92,perid.call=.92)
names(mc)
mc$nohwe
-mc <- check.marker(data=srdta at gtdata[,1:100],call=0.95,perid.call=0.9,maf=0.02,minconcordance=0.9,fdr=0.1,redundant="all",ibs.mrk=0)
+mc <- check.marker(data=srdta at gtdata[,1:100],call=0.95,perid.call=0.9,
+ maf=0.02,minconcordance=0.9,fdr=0.1,redundant="all",ibs.mrk=0)
summary(mc)
HWE.show(data=srdta,snps=mc$nohwe)
plot(mc)
Modified: pkg/GenABEL/man/convert.snp.affymetrix.Rd
===================================================================
--- pkg/GenABEL/man/convert.snp.affymetrix.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/convert.snp.affymetrix.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -86,7 +86,8 @@
}
\examples{
\dontrun{
- convert.snp.affymetrix(dir="where_is_our_aff_files", map="map_file", outfile="output.raw", skipaffym=3)
+ convert.snp.affymetrix(dir="where_is_our_aff_files", map="map_file",
+ outfile="output.raw", skipaffym=3)
}
}
\keyword{IO}
Modified: pkg/GenABEL/man/convert.snp.mach.Rd
===================================================================
--- pkg/GenABEL/man/convert.snp.mach.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/convert.snp.mach.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -6,7 +6,8 @@
(NOT recommended)
}
\usage{
-convert.snp.mach(pedfile, mapfile, infofile, outfile, quality = 0.9, column.quality = 7, strand = "+", ...)
+convert.snp.mach(pedfile, mapfile, infofile, outfile, quality = 0.9,
+ column.quality = 7, strand = "+", ...)
}
\arguments{
\item{pedfile}{
Modified: pkg/GenABEL/man/egscore.old.Rd
===================================================================
--- pkg/GenABEL/man/egscore.old.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/egscore.old.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -6,7 +6,8 @@
adjusted for possible stratification by principal components.
}
\usage{
-egscore.old(formula,data,snpsubset,idsubset,kinship.matrix,naxes=3,strata,times=1,quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0)
+egscore.old(formula,data,snpsubset,idsubset,kinship.matrix,naxes=3,strata,
+ times=1,quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0)
}
\arguments{
\item{formula}{Formula describing fixed effects to be used in analysis, e.g.
Modified: pkg/GenABEL/man/emp.qtscore.Rd
===================================================================
--- pkg/GenABEL/man/emp.qtscore.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/emp.qtscore.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -6,8 +6,8 @@
function is \code{\link{qtscore}}.
}
\usage{
-emp.qtscore(formula , data, snpsubset, idsubset, strata, trait.type="gaussian", times = 200,
- quiet=FALSE, bcast = 10)
+emp.qtscore(formula , data, snpsubset, idsubset, strata, trait.type="gaussian",
+ times = 200, quiet=FALSE, bcast = 10)
}
\arguments{
All arguments are the same as in and passed intact to the \code{\link{qtscore}}.
Modified: pkg/GenABEL/man/export.merlin.Rd
===================================================================
--- pkg/GenABEL/man/export.merlin.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/export.merlin.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -5,9 +5,10 @@
Exports GenABEL data to Merlin and other pedigree formats
}
\usage{
- export.merlin(data, pedfile = "merlin.ped", datafile = "merlin.dat", mapfile = "merlin.map",
- format = "merlin", fixstrand = "no", extendedmap = TRUE, traits = 1, order = TRUE,
- stepids = 100, dpieceFun = "new")
+ export.merlin(data, pedfile = "merlin.ped", datafile = "merlin.dat",
+ mapfile = "merlin.map", format = "merlin", fixstrand = "no",
+ extendedmap = TRUE, traits = 1, order = TRUE, stepids = 100,
+ dpieceFun = "new")
}
%- maybe also 'usage' for other objects documented here.
\arguments{
Modified: pkg/GenABEL/man/hom.old.Rd
===================================================================
--- pkg/GenABEL/man/hom.old.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/hom.old.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -67,7 +67,8 @@
h <- hom(ge03d2[,c(1:100)])
homsem <- h[,"Hom"]*(1-h[,"Hom"])/h[,"NoMeasured"]
plot(h[,"Hom"],homsem)
-# wrong analysis: one should use all people (for right frequency) and markers (for right F) available!
+# wrong analysis: one should use all people (for right frequency)
+# and markers (for right F) available!
h <- hom(ge03d2[,c(1:10)])
h
}
Modified: pkg/GenABEL/man/ibs.old.Rd
===================================================================
--- pkg/GenABEL/man/ibs.old.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/ibs.old.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -59,7 +59,8 @@
a <- ibs(data=ge03d2c,ids=c(1:10),snps=c(1:1000))
a
# compute IBS based on a random sample of 1000 autosomal marker
-a <- ibs(ge03d2c,snps=sample(ge03d2c at gtdata@snpnames[ge03d2c at gtdata@chromosome!="X"],1000,replace=FALSE),weight="freq")
+a <- ibs(ge03d2c,snps=sample(ge03d2c at gtdata@snpnames[ge03d2c at gtdata@chromosome!="X"],
+ 1000,replace=FALSE),weight="freq")
mds <- cmdscale(as.dist(1-a))
plot(mds)
# identify smaller cluster of outliers
Modified: pkg/GenABEL/man/merge.snp.data.Rd
===================================================================
--- pkg/GenABEL/man/merge.snp.data.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/merge.snp.data.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -6,7 +6,8 @@
}
\usage{
\method{merge}{snp.data}(x, y, ... , error_amount = 1e+06, replacena = TRUE,
- forcestranduse = FALSE, sort = TRUE, intersected_snps_only = FALSE)
+ forcestranduse = FALSE, sort = TRUE,
+ intersected_snps_only = FALSE)
}
\arguments{
\item{x}{the first object of \code{\link{snp.data-class}}}
Modified: pkg/GenABEL/man/mmscore.Rd
===================================================================
--- pkg/GenABEL/man/mmscore.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/mmscore.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -6,7 +6,8 @@
in samples of related individuals
}
\usage{
-mmscore(h2object,data,snpsubset,idsubset,strata,times=1,quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0,cppFun="new")
+mmscore(h2object,data,snpsubset,idsubset,strata,times=1,quiet=FALSE,
+ bcast=10,clambda=TRUE,propPs=1.0,cppFun="new")
}
\arguments{
\item{h2object}{An object returned by \code{\link{polygenic}} polygenic mixed model analysis
Modified: pkg/GenABEL/man/npsubtreated.Rd
===================================================================
--- pkg/GenABEL/man/npsubtreated.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/npsubtreated.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -77,11 +77,14 @@
# see what comes out of regression
# analysis of true value
summary(lm(y.true~sex+age+gt,data=x))
-# ignore treatment (as a rule, betas are underestimated; on average, power goes down)
+# ignore treatment (as a rule, betas are underestimated;
+# on average, power goes down)
summary(lm(y.obs~sex+age+gt,data=x))
-# treatment as covariate (as a rule, betas are underestimated; on average, power goes down)
+# treatment as covariate (as a rule, betas are underestimated;
+# on average, power goes down)
summary(lm(y.obs~sex+age+gt+medication,data=x))
-# analyse "imputed" trait (as a rule betas are better; power approaches that of analysis of "true" trait)
+# analyse "imputed" trait (as a rule betas are better; power
+# approaches that of analysis of "true" trait)
summary(lm(imptra~sex+age+gt,data=x))
}
\keyword{robust}
Modified: pkg/GenABEL/man/plot.check.marker.Rd
===================================================================
--- pkg/GenABEL/man/plot.check.marker.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/plot.check.marker.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -39,7 +39,8 @@
}
\examples{
data(srdta)
-mc <- check.marker(data=srdta at gtdata[,1:100],redundant="all",maf=0.01,minconcordance=0.9,fdr=.1,ibs.mrk=0)
+mc <- check.marker(data=srdta at gtdata[,1:100],redundant="all",maf=0.01,
+ minconcordance=0.9,fdr=.1,ibs.mrk=0)
mc <- check.marker(data=srdta at gtdata[,1:100],maf=0.01,fdr=.1,ibs.mrk=0)
plot(mc)
mc1 <- snp.subset(mc,snps=srdta at gtdata@snpnames[20:40])
Modified: pkg/GenABEL/man/scan.haplo.2D.Rd
===================================================================
--- pkg/GenABEL/man/scan.haplo.2D.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/scan.haplo.2D.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -7,7 +7,8 @@
and presents output as \code{\link{scan.gwaa.2D-class}} object
}
\usage{
-scan.haplo.2D(formula, data, snpsubset, idsubset, bcast = 10, simulate=FALSE, trait.type, ...)
+scan.haplo.2D(formula, data, snpsubset, idsubset, bcast = 10,
+ simulate=FALSE, trait.type, ...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
Modified: pkg/GenABEL/man/scan.haplo.Rd
===================================================================
--- pkg/GenABEL/man/scan.haplo.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/scan.haplo.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -7,7 +7,8 @@
\code{\link{scan.gwaa-class}} data object
}
\usage{
-scan.haplo(formula, data, snpsubset, idsubset, n.slide = 2, bcast = 10, simulate=FALSE, trait.type, ...)
+scan.haplo(formula, data, snpsubset, idsubset, n.slide = 2, bcast = 10,
+ simulate=FALSE, trait.type, ...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
Modified: pkg/GenABEL/man/snp.subset.Rd
===================================================================
--- pkg/GenABEL/man/snp.subset.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/snp.subset.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -27,7 +27,8 @@
\examples{
data(srdta)
# processing check.marker object
-#mc <- check.marker(data=srdta at gtdata[,1:100],redundant="all",maf=0.01,minconcordance=0.9,fdr=.1,ibs.mrk=0)
+#mc <- check.marker(data=srdta at gtdata[,1:100],redundant="all",maf=0.01,
+# minconcordance=0.9,fdr=.1,ibs.mrk=0)
mc <- check.marker(data=srdta at gtdata[,1:100],maf=0.01,fdr=.1,ibs.mrk=0)
summary(mc)
#plot(mc)
Modified: pkg/GenABEL/man/srdta.Rd
===================================================================
--- pkg/GenABEL/man/srdta.Rd 2013-05-15 10:00:36 UTC (rev 1217)
+++ pkg/GenABEL/man/srdta.Rd 2013-05-16 12:41:40 UTC (rev 1218)
@@ -34,7 +34,8 @@
data(srdta)
# truncate the data to make the example faster
srdta <- srdta[seq(from=1,to=nids(srdta),by=2),seq(from=1,to=nsnps(srdta),by=2)]
-mc <- check.marker(data=gtdata(srdta)[,1:100],redundant="all",maf=0.01,minconcordance=0.9,fdr=.1,ibs.mrk=0)
+mc <- check.marker(data=gtdata(srdta)[,1:100],redundant="all",
+ maf=0.01,minconcordance=0.9,fdr=.1,ibs.mrk=0)
plot(mc)
check.trait(names(phdata(srdta)),srdta)
}
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