[Genabel-commits] r928 - pkg/GenABEL/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jul 6 07:14:24 CEST 2012
Author: nd_0001
Date: 2012-07-06 07:14:23 +0200 (Fri, 06 Jul 2012)
New Revision: 928
Added:
pkg/GenABEL/man/PGC.Rd
Removed:
pkg/GenABEL/man/grammar.old.Rd
Modified:
pkg/GenABEL/man/impute2databel.Rd
Log:
killed grammar.old.Rd;added PGC.Rd function
Added: pkg/GenABEL/man/PGC.Rd
===================================================================
--- pkg/GenABEL/man/PGC.Rd (rev 0)
+++ pkg/GenABEL/man/PGC.Rd 2012-07-06 05:14:23 UTC (rev 928)
@@ -0,0 +1,50 @@
+\name{PGC}
+\alias{PGC}
+\title{Polynomial genomic control}
+\usage{
+ PGC(data, method = "regress", p, df, pol.d = 3,
+ plot = TRUE, index.filter = 0, start.corr = FALSE)
+}
+\arguments{
+ \item{data}{Input vector of Chi square statistic}
+
+ \item{method}{Function of error to be optimized. Can be
+ "regress", "median" or "ks.test"}
+
+ \item{p}{Input vector of allele frequencies}
+
+ \item{df}{Number of dergees of freedom}
+
+ \item{pol.d}{Polinom degree}
+
+ \item{plot}{If true, functon makes plot of lambda from
+ allele frequencies}
+
+ \item{start.corr}{For regress method use it only when you
+ want to make calculations faster}
+
+ \item{index.filter}{Index of variables in data vector,
+ that will be used in analysis, if zero - all variables
+ will be used}
+}
+\value{
+ A list with values \item {data} output vector corrected
+ Chi square statistic \item {b} polinom coefficients
+}
+\description{
+ This function estimates the genomic controls for diffrent
+ model and degrees of freedom, using polinom function.
+ Polinomic coefficients are estimated by optimizing
+ diffrent error functions: regress, median and ks.test.
+}
+\examples{
+a=1
+b=1
+a+b
+}
+\author{
+ Yakov Tsepilov
+}
+\keyword{'}
+\keyword{htest}
+
Deleted: pkg/GenABEL/man/grammar.old.Rd
===================================================================
--- pkg/GenABEL/man/grammar.old.Rd 2012-07-06 05:13:36 UTC (rev 927)
+++ pkg/GenABEL/man/grammar.old.Rd 2012-07-06 05:14:23 UTC (rev 928)
@@ -1,106 +0,0 @@
-\name{grammar.old}
-\alias{grammar.old}
-\title{Approximate score test for association in related people}
-\description{
-Fast approximate score test for association between a trait and genetic polymorphism,
-in samples of related individuals. When used with argument "times=1", it is equivalent to
-running \code{\link{qtscore}} on "environmental residuals" from \code{\link{polygenic}}.
-However, it does not produce correct results with permutations, because the raw
-trait values, which are not exchangeable, are permuted. Use \code{\link{qtscore}}
-on "environmental residuals" when you want to have empirical GW significance with grammar.old
-method.
-}
-\usage{
-grammar.old(h2object,data,snpsubset,idsubset,strata,times=1,quiet=FALSE,bcast=10,clambda=FALSE,propPs=1.0)
-}
-\arguments{
- \item{h2object}{An object returned by \code{\link{polygenic}} polygenic mixed model analysis
- routine. The sub-objects used are measuredIDs, residualY, h2an\$estimates (last element,
- total variance, only), and InvSigma.
- One can supply grammar.old with a fake h2object, containing these list elements.
- }
- \item{data}{An object of \code{\link{gwaa.data-class}}}
- \item{snpsubset}{Index, character or logical vector with subset of SNPs to run analysis on.
- If missing, all SNPs from \code{data} are used for analysis.}
- \item{idsubset}{Index, character or logical vector with subset of IDs to run analysis on.
- If missing, all people from \code{data/cc} are used for analysis.}
- \item{strata}{Stratification variable. If provieded, scores are computed within strata and
- then added up.}
- \item{times}{If more then one, the number of replicas to be used in derivation of
- empirical genome-wide significance. NOTE: do not use times > 1
- unless you are really sure you understand what you are doing!
- }
- \item{quiet}{do not print warning messages}
- \item{bcast}{If the argument times > 1, progress is reported once in bcast replicas}
- \item{clambda}{If inflation facor Lambda is estimated as lower then one, this parameter
- controls if the original P1df (clambda=TRUE) to be reported in Pc1df,
- or the original 1df statistics is to be multiplied onto this "deflation"
- factor (clambda=FALSE). With grammar.old, Lambda is expected ot be less than 1.
- If a numeric value is provided, it is used as a correction factor.}
- \item{propPs}{proportion of non-corrected P-values used to estimate the inflation factor Lambda,
- passed directly to the \code{\link{estlambda}}}
-}
-\details{
- Approximate score test is performed using the formula
-
- \deqn{
- \sigma^4 \frac{((G-E[G]) V^{-1} residualY)^2}{(G-E[G]) (G-E[G])}
- }{
- sigma^4 (((G-E[G]) V^(-1) residualY)^2)/((G-E[G]) (G-E[G]))
- }
-
- where $sigma^4$ is the square of the residual
- variance, $G$ is the vector of genotypes (coded 0, 1, 2) and $E[G]$ is
- a vector of (strata-specific) mean genotypic values;
- \eqn{V^{-1}}{V^(-1)}
- is the
- InvSigma and $residualY$ are residuals from the trait analysis
- with \code{\link{polygenic}} procedure.
-
- Compared to score test implemented in \code{\link{mmscore}}, grammar.old
- test is faster and computation time grows only linearly with the
- number of subjects (with \code{\link{mmscore}} this relation is
- quadratic). While raw P1df from grammar.old are not quite correct,
- the GC p-values correspond very closely to these from the \code{\link{mmscore}}.
-}
-\value{
- Object of class \code{\link{scan.gwaa-class}}; only 1 d.f. test is
- implemented currently.
-}
-\references{
-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.
-
-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.
-}
-\author{Yurii Aulchenko}
-%\note{}
-\seealso{
-\code{\link{grammar.old}},
-\code{\link{qtscore}},
-\code{\link{plot.scan.gwaa}},
-\code{\link{scan.gwaa-class}}
-}
-\examples{
-# ge03d2.clean is rather bad data set to demonstrate grammar.old,
-# because this is a population-based study
-data(ge03d2.clean)
-#take half for speed
-ge03d2.clean <- ge03d2.clean[1:100,]
-gkin <- ibs(ge03d2.clean,w="freq")
-h2ht <- polygenic(height ~ sex + age,kin=gkin,ge03d2.clean)
-h2ht$est
-# can use "grammar.old", but ...
-a <- grammar.old(h2ht,data=ge03d2.clean)
-# ... use rather qtscore (note clam=FALSE), which is a better alternative for the same thing
-a <- qtscore(h2ht$pgres,data=ge03d2.clean,clam=FALSE)
-# compare to GC:
-b <- qtscore(height ~ sex + age,data=ge03d2.clean)
-plot(b,df="Pc1df")
-add.plot(a,df="Pc1df")
-# relatively large difference is due to high heritability
-# note that locus at chromosome 2 should indeed be there...
-}
-\keyword{htest}% at least one, from doc/KEYWORDS
Modified: pkg/GenABEL/man/impute2databel.Rd
===================================================================
--- pkg/GenABEL/man/impute2databel.Rd 2012-07-06 05:13:36 UTC (rev 927)
+++ pkg/GenABEL/man/impute2databel.Rd 2012-07-06 05:14:23 UTC (rev 928)
@@ -24,8 +24,8 @@
this function converts IMPUTE-imputed files to DatABEL
(filevector) format containing estimated dosages. After
conversion, two files (outfile.fvi and outfile.fvd),
- corresponding to single filevector object, will appear on
- the disk; 'databel-class' object connected to these files
- will be returned to R.
+ corresponding to a single filevector object, will appear
+ on the disk; a 'databel-class' object connected to these
+ files will be returned to R.
}
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