[Genabel-commits] r1254 - in pkg/GenABEL: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jun 29 12:49:39 CEST 2013
Author: yurii
Date: 2013-06-29 12:49:38 +0200 (Sat, 29 Jun 2013)
New Revision: 1254
Modified:
pkg/GenABEL/CHANGES.LOG
pkg/GenABEL/DESCRIPTION
pkg/GenABEL/R/GenABEL.R
pkg/GenABEL/R/impute2databel.R
pkg/GenABEL/R/mach2databel.R
pkg/GenABEL/R/minimac2databel.R
pkg/GenABEL/R/polygenic.R
pkg/GenABEL/R/zzz.R
pkg/GenABEL/man/GenABEL.Rd
pkg/GenABEL/man/export.plink.Rd
pkg/GenABEL/man/impute2databel.Rd
pkg/GenABEL/man/mach2databel.Rd
pkg/GenABEL/man/polygenic.Rd
Log:
ref for Grammar+; data types for *2databel; version to 1.7-7
Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/CHANGES.LOG 2013-06-29 10:49:38 UTC (rev 1254)
@@ -1,5 +1,12 @@
-*** v. 1.7-
+*** v. 1.7-7
+(2013.06.29)
+Added references for Grammar+ transformation
+
+Allowed for user-specified output data type in '*2databel' functions
+
+Changed version number to 1.7-7
+
(2013.06.06)
Two new functions added: LiLog() and palinear2LiLog() for the
estimation of logistic beta's from a linear regression. Thanks to
Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/DESCRIPTION 2013-06-29 10:49:38 UTC (rev 1254)
@@ -1,8 +1,8 @@
Package: GenABEL
Type: Package
Title: genome-wide SNP association analysis
-Version: 1.7-6
-Date: 2013-05-16
+Version: 1.7-7
+Date: 2013-06-29
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/GenABEL.R
===================================================================
--- pkg/GenABEL/R/GenABEL.R 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/R/GenABEL.R 2013-06-29 10:49:38 UTC (rev 1254)
@@ -112,7 +112,8 @@
#' \code{\link{polygenic}} (heritability analysis),
#' \code{\link{polygenic_hglm}} (another function for heritability analysis),
#' \code{\link{mmscore}} (score test of Chen and Abecasis),
-#' \code{\link{grammar}} (grammar test of Aulchenko et al.).
+#' \code{\link{grammar}} (grammar, grammar-gc, and garmmar-gamma tests of
+#' Aulchenko et al., Amin et al., and Svishcheva et al.).
#'
#' For functions facilitating construction of tables for your manuscript, see
#' \code{\link{descriptives.marker}},
@@ -177,6 +178,12 @@
#' variance components-based method for whole-genome association analysis.
#' Nature Genetics. 2012 44:1166-1170. doi:10.1038/ng.2410
#'
+#' for GRAMMAR+ transformation
+#'
+#' Belonogova NM, Svishcheva GR, van Duijn CM, Aulchenko YS, Axenovich TI (2013)
+#' Region-Based Association Analysis of Human Quantitative Traits in Related Individuals.
+#' PLoS ONE 8(6): e65395. doi:10.1371/journal.pone.0065395
+#'
#' If you used \code{\link{mmscore}}, please cite
#'
#' Chen WM, Abecasis GR. Family-based association tests for genome-wide association
Modified: pkg/GenABEL/R/impute2databel.R
===================================================================
--- pkg/GenABEL/R/impute2databel.R 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/R/impute2databel.R 2013-06-29 10:49:38 UTC (rev 1254)
@@ -12,6 +12,8 @@
#' @param outfile output file name
#' @param makeprob whether probability-files are also to be arranged
#' @param old for developers' use only
+#' @param dataOutType the output data type, either "FLOAT" or "DOUBLE" (or
+#' other DatABEL/filevector type)
#'
#' @return 'databel-class' object
#'
@@ -19,7 +21,7 @@
impute2databel <- function(genofile, samplefile, outfile,
- makeprob=TRUE, old=FALSE)
+ makeprob = TRUE, old = FALSE, dataOutType = "FLOAT")
{
if (!require(DatABEL))
stop("this function requires the DatABEL package to be installed")
@@ -36,7 +38,7 @@
## colnames=tmpname,
## rownames=2,skipcols=5,
## #skiprows,
- ## transpose=TRUE,R_matrix=FALSE,type="FLOAT")
+ ## transpose=TRUE,R_matrix=FALSE,type = dataOutType)
## else
tmpname <- get_temporary_file_name()
tmp_fv <- text2databel(infile=genofile,
@@ -46,7 +48,7 @@
## skiprows,
transpose=TRUE,
R_matrix=FALSE,
- type="FLOAT")
+ type = dataOutType)
if ((dim(tmp_fv)[1] %% 3) != 0)
stop("strange data in IMPUTE geno file: ",
"number of columns - 5 not dividable by 3")
@@ -64,7 +66,7 @@
## dosefile <- make_empty_fvf(paste(outfile, ".dose", sep=""),
## nvariables = dim(tmp_fv)[2],
## nobservations = round(dim(tmp_fv)[1]/3),
- ## type = "FLOAT")
+ ## type = dataOutType)
## print(dimnames(tmp_fv)[[2]])
## print(dim(tmp_fv))
@@ -93,7 +95,7 @@
prob=get("SNP"),
outclass="databel",
outfile=paste(outfile, ".dose", sep=""),
- type="FLOAT",
+ type=dataOutType,
transpose=FALSE)
if (makeprob) {
stop("makeprob is not possible with 'old' style")
Modified: pkg/GenABEL/R/mach2databel.R
===================================================================
--- pkg/GenABEL/R/mach2databel.R 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/R/mach2databel.R 2013-06-29 10:49:38 UTC (rev 1254)
@@ -11,6 +11,8 @@
#' @param outfile output file name
#' @param isprobfile whether imputedgenofile is a prob-file
#' (default is FALSE, that is dose-file assumed)
+#' @param dataOutType the output data type, either "FLOAT" or "DOUBLE" (or
+#' other DatABEL/filevector type)
#'
#' @return databel-class object
#'
@@ -21,7 +23,8 @@
#'
-mach2databel <- function(imputedgenofile,mlinfofile,outfile,isprobfile=FALSE)
+mach2databel <- function(imputedgenofile,mlinfofile,outfile,
+ isprobfile=FALSE, dataOutType = "FLOAT")
{
if (!require(DatABEL))
stop("this function requires DatABEL package to be installed")
@@ -52,12 +55,14 @@
colnames=tmpname,
rownames=1,skipcols=2,
#skiprows,
- transpose=FALSE,R_matrix=FALSE,type="FLOAT",readonly=FALSE)
+ transpose=FALSE,R_matrix=FALSE,
+ type = dataOutType, readonly = FALSE)
else
dfaobj <- text2databel(infile=imputedgenofile,outfile=outfile,
rownames=1,skipcols=2,
#skiprows,
- transpose=FALSE,R_matrix=FALSE,type="FLOAT",readonly=FALSE)
+ transpose=FALSE,R_matrix=FALSE,
+ type = dataOutType, readonly = FALSE)
dnames <- get_dimnames(dfaobj)
subjs <- dnames[[1]]
@@ -76,4 +81,4 @@
#disconnect(dfaobj)
#connect(dfaobj)
return(dfaobj)
-}
\ No newline at end of file
+}
Modified: pkg/GenABEL/R/minimac2databel.R
===================================================================
--- pkg/GenABEL/R/minimac2databel.R 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/R/minimac2databel.R 2013-06-29 10:49:38 UTC (rev 1254)
@@ -14,6 +14,8 @@
#' @param outfile output file name
#' @param cachesizeMb cache size for the resulting 'databel-class'
#' object (gets passed directly to the \code{text2databel()} function)
+#' @param dataOutType the output data type, either "FLOAT" or "DOUBLE" (or
+#' other DatABEL/filevector type)
#'
#' @return databel-class object
#'
@@ -24,7 +26,8 @@
#'
-minimac2databel <- function(imputedgenofile, infofile, outfile, cachesizeMb=64)
+minimac2databel <- function(imputedgenofile, infofile, outfile,
+ cachesizeMb=64, dataOutType = "FLOAT")
{
if (!require(DatABEL))
stop("This function requires DatABEL package to be installed")
@@ -52,7 +55,7 @@
skipcols=2,
transpose=FALSE,
R_matrix=FALSE,
- type="FLOAT",
+ type = dataOutType,
readonly=FALSE,
cachesizeMb=cachesizeMb)
else
@@ -62,7 +65,7 @@
skipcols=2,
transpose=FALSE,
R_matrix=FALSE,
- type="FLOAT",
+ type = dataOutType,
readonly=FALSE,
cachesizeMb=cachesizeMb)
Modified: pkg/GenABEL/R/polygenic.R
===================================================================
--- pkg/GenABEL/R/polygenic.R 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/R/polygenic.R 2013-06-29 10:49:38 UTC (rev 1254)
@@ -105,7 +105,7 @@
#' \item{pgresidualY}{Environmental residuals from analysis, based on covariate effects
#' and predicted breeding value.
#' }
-#' \item{grresidualY}{GRAMMAR-transform trait transformation}
+#' \item{grresidualY}{GRAMMAR+ transformed trait residuals}
#' \item{grammarGamma}{list with GRAMMAR-gamma correction factors}
#' \item{InvSigma}{Inverse of the variance-covariance matrix, computed at the
#' MLEs -- these are used in \code{\link{mmscore}} and \code{\link{grammar}}
@@ -121,15 +121,29 @@
#' traits: variance components without matrix inversion. Biometrics
#' 46, 399-413.
#'
+#' 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.
#'
-#' G. Svischeva et al. (in preparation)
+#' 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
+#'
+#' for GRAMMAR+ transformation
+#'
+#' Belonogova NM, Svishcheva GR, van Duijn CM, Aulchenko YS, Axenovich TI (2013)
+#' Region-Based Association Analysis of Human Quantitative Traits in Related Individuals.
+#' PLoS ONE 8(6): e65395. doi:10.1371/journal.pone.0065395
+#'
#' @author Yurii Aulchenko, Gulnara Svischeva
#'
#' @note
Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/R/zzz.R 2013-06-29 10:49:38 UTC (rev 1254)
@@ -4,8 +4,8 @@
#pkgDescription <- packageDescription(pkg)
#pkgVersion <- pkgDescription$Version
#pkgDate <- pkgDescription$Date
- pkgVersion <- "1.7-6"
- pkgDate <- "May 16, 2013"
+ pkgVersion <- "1.7-7"
+ pkgDate <- "June 29, 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 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/man/GenABEL.Rd 2013-06-29 10:49:38 UTC (rev 1254)
@@ -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
@@ -126,7 +126,9 @@
(heritability analysis), \code{\link{polygenic_hglm}}
(another function for heritability analysis),
\code{\link{mmscore}} (score test of Chen and Abecasis),
- \code{\link{grammar}} (grammar test of Aulchenko et al.).
+ \code{\link{grammar}} (grammar, grammar-gc, and
+ garmmar-gamma tests of Aulchenko et al., Amin et al., and
+ Svishcheva et al.).
For functions facilitating construction of tables for
your manuscript, see \code{\link{descriptives.marker}},
@@ -203,6 +205,13 @@
whole-genome association analysis. Nature Genetics. 2012
44:1166-1170. doi:10.1038/ng.2410
+ for GRAMMAR+ transformation
+
+ Belonogova NM, Svishcheva GR, van Duijn CM, Aulchenko YS,
+ Axenovich TI (2013) Region-Based Association Analysis of
+ Human Quantitative Traits in Related Individuals. PLoS
+ ONE 8(6): e65395. doi:10.1371/journal.pone.0065395
+
If you used \code{\link{mmscore}}, please cite
Chen WM, Abecasis GR. Family-based association tests for
Modified: pkg/GenABEL/man/export.plink.Rd
===================================================================
--- pkg/GenABEL/man/export.plink.Rd 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/man/export.plink.Rd 2013-06-29 10:49:38 UTC (rev 1254)
@@ -8,30 +8,30 @@
}
\arguments{
\item{data}{GenABEL data object of 'gwaa.data'-class to
- be exported}
+ be exported.}
\item{filebasename}{base file name for exported data,
extensions '.ped', '.map' and '.phe' (for phenotype file)
- are added for specific output files}
+ are added for specific output files.}
\item{phenotypes}{NULL (no phenotypes exported), "all"
- for all phenotypes or a vector of character with names of
- phneotypes to be exported}
+ (default) for all phenotypes or a vector of character
+ with names of phenotypes to be exported.}
- \item{transpose}{if FALSE, regular 'tped' files produced,
- else 'ped' files are produced}
+ \item{transpose}{if FALSE (default), 'tped' files will be
+ produced, else 'ped' files are produced.}
- \item{export012na}{if true, export in numeric (0, 1, 2,
- NA) format (as opposed to ATGC format)}
+ \item{export012na}{if TRUE, export in numeric (0, 1, 2,
+ NA) format, as opposed to ATGC format (default: FALSE).}
\item{...}{arguments passed to
- \code{\link{export.merlin}}}
+ \code{\link{export.merlin}}.}
}
\description{
Export GenABEL data in PLINK format. This function is a
- simple wrapper to \code{\link{export.merlin}} function
- with specific arguments + few lines of code to export
- phenotypes
+ simple wrapper to the \code{\link{export.merlin}}
+ function with specific arguments + few lines of code to
+ export phenotypes
}
\author{
Yurii Aulchenko
Modified: pkg/GenABEL/man/impute2databel.Rd
===================================================================
--- pkg/GenABEL/man/impute2databel.Rd 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/man/impute2databel.Rd 2013-06-29 10:49:38 UTC (rev 1254)
@@ -3,7 +3,7 @@
\title{converts IMPUTE-imputed files to DatABEL (filevector) format}
\usage{
impute2databel(genofile, samplefile, outfile,
- makeprob = TRUE, old = FALSE)
+ makeprob = TRUE, old = FALSE, dataOutType = "FLOAT")
}
\arguments{
\item{genofile}{IMPUTE genotype file name}
@@ -12,10 +12,13 @@
\item{outfile}{output file name}
- \item{makeprob}{wheather probability-files are also to be
+ \item{makeprob}{whether probability-files are also to be
arranged}
- \item{old}{for developers' use}
+ \item{old}{for developers' use only}
+
+ \item{dataOutType}{the output data type, either "FLOAT"
+ or "DOUBLE" (or other DatABEL/filevector type)}
}
\value{
'databel-class' object
Modified: pkg/GenABEL/man/mach2databel.Rd
===================================================================
--- pkg/GenABEL/man/mach2databel.Rd 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/man/mach2databel.Rd 2013-06-29 10:49:38 UTC (rev 1254)
@@ -3,7 +3,7 @@
\title{converts MACH-imputed files to DatABEL (filevector) format}
\usage{
mach2databel(imputedgenofile, mlinfofile, outfile,
- isprobfile = FALSE)
+ isprobfile = FALSE, dataOutType = "FLOAT")
}
\arguments{
\item{imputedgenofile}{MACH mldose (or mlprob) file name}
@@ -14,6 +14,9 @@
\item{isprobfile}{whether imputedgenofile is a prob-file
(default is FALSE, that is dose-file assumed)}
+
+ \item{dataOutType}{the output data type, either "FLOAT"
+ or "DOUBLE" (or other DatABEL/filevector type)}
}
\value{
databel-class object
Modified: pkg/GenABEL/man/polygenic.Rd
===================================================================
--- pkg/GenABEL/man/polygenic.Rd 2013-06-29 10:45:59 UTC (rev 1253)
+++ pkg/GenABEL/man/polygenic.Rd 2013-06-29 10:49:38 UTC (rev 1254)
@@ -100,11 +100,11 @@
"environmental residuals"!}
\item{pgresidualY}{Environmental residuals from analysis,
based on covariate effects and predicted breeding value.
- } \item{grresidualY}{GRAMMAR-transform trait
- transformation} \item{grammarGamma}{list with
- GRAMMAR-gamma correction factors} \item{InvSigma}{Inverse
- of the variance-covariance matrix, computed at the MLEs
- -- these are used in \code{\link{mmscore}} and
+ } \item{grresidualY}{GRAMMAR+ transformed trait
+ residuals} \item{grammarGamma}{list with GRAMMAR-gamma
+ correction factors} \item{InvSigma}{Inverse of the
+ variance-covariance matrix, computed at the MLEs -- these
+ are used in \code{\link{mmscore}} and
\code{\link{grammar}} functions.} \item{call}{The details
of call} \item{measuredIDs}{Logical values for IDs who
were used in analysis (traits and all covariates
@@ -203,17 +203,33 @@
quantitative traits: variance components without matrix
inversion. Biometrics 46, 399-413.
+ 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.
- G. Svischeva et al. (in preparation)
+ 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
+
+ for GRAMMAR+ transformation
+
+ Belonogova NM, Svishcheva GR, van Duijn CM, Aulchenko YS,
+ Axenovich TI (2013) Region-Based Association Analysis of
+ Human Quantitative Traits in Related Individuals. PLoS
+ ONE 8(6): e65395. doi:10.1371/journal.pone.0065395
}
\seealso{
\code{\link{polygenic_hglm}}, \code{\link{mmscore}},
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