[Genabel-commits] r977 - in pkg/GenABEL: R man

[noreply at r-forge.r-project.org]

Author: nd_0001
Date: 2012-10-11 12:41:09 +0200 (Thu, 11 Oct 2012)
New Revision: 977

Modified:
   pkg/GenABEL/R/estlambda.R
   pkg/GenABEL/R/zUtil.R
   pkg/GenABEL/man/GenABEL.Rd
   pkg/GenABEL/man/estlambda.Rd
Log:
a few changes in estlambda

Modified: pkg/GenABEL/R/estlambda.R
===================================================================
--- pkg/GenABEL/R/estlambda.R	2012-10-06 11:27:18 UTC (rev 976)
+++ pkg/GenABEL/R/estlambda.R	2012-10-11 10:41:09 UTC (rev 977)
@@ -9,8 +9,7 @@
 #' 
 #' 
 #' @param data A vector of reals. If all are <=1, it is assumed that this is a
-#'   vector of P-values, else it is treated as a vector of chi-squares with 1
-#'   d.f.
+#'   vector of P-values, else it is treated as a vector of chi-squares
 #' @param plot Wether the prot should be presented
 #' @param proportion The proportion of lowest P (Chi2) to be used when
 #'   estimating the inflation factor Lambda
@@ -18,6 +17,7 @@
 #'   Lambda estimation
 #' @param filter if the test statistics with 0-value of chi-square should be
 #'   excluded prior to estimation of Lambda
+#' @param df Number of degrees of freedom
 #' @param ... arguments passed to \code{\link{plot}} function
 #' @return A list with elements \item{estimate}{Estimate of Lambda}
 #'   \item{se}{Standard error of the estimate}
@@ -36,7 +36,7 @@
 #' lambda(a)
 #' 
 "estlambda" <-
-		function(data,plot = FALSE, proportion=1.0, method="regression", filter=TRUE, ... ) {
+		function(data,plot = FALSE, proportion=1.0, method="regression", filter=TRUE, df=1,... ) {
 	data <- data[which(!is.na(data))]
 	if (proportion>1.0 || proportion<=0) 
 		stop("proportion argument should be greater then zero and less than or equal to one")
@@ -62,7 +62,7 @@
 	}
 	data <- sort(data)
 	ppoi <- ppoints(data)
-	ppoi <- sort(qchisq(1-ppoi,1))
+	ppoi <- sort(qchisq(1-ppoi,df))
 	data <- data[1:ntp]
 	ppoi <- ppoi[1:ntp]
 #	s <- summary(lm(data~offset(ppoi)))$coeff
@@ -74,11 +74,11 @@
 		out$estimate <- s[1,1]
 		out$se <- s[1,2]
 	} else if (method=="median") {
-		out$estimate <- median(data,na.rm=TRUE)/qchisq(0.5,1)
+		out$estimate <- median(data,na.rm=TRUE)/qchisq(0.5,df)
 		out$se <- NA
 	} else if (method=="KS") {
 		limits <- c(0.5,100)
-		out$estimate <- estLambdaKS(data,limits=limits)
+		out$estimate <- estLambdaKS(data,limits=limits,df=df)
 		if ( abs(out$estimate-limits[1])<1e-4 || abs(out$estimate-limits[2])<1e-4 ) 
 			warning("using method='KS' lambda too close to limits, use other method")
 		out$se <- NA

Modified: pkg/GenABEL/R/zUtil.R
===================================================================
--- pkg/GenABEL/R/zUtil.R	2012-10-06 11:27:18 UTC (rev 976)
+++ pkg/GenABEL/R/zUtil.R	2012-10-11 10:41:09 UTC (rev 977)
@@ -3,9 +3,9 @@
 	ksT <- ks.test(chi2values/lambda, ... )$stat
 	return( ksT )
 }
-estLambdaKS <- function(chi2values,limits=c(0.5,100)) {
+estLambdaKS <- function(chi2values,limits=c(0.5,100),df=1) {
 	iniLambda <- 1
-	optRes <- optimize(lossFunctionLambdaKS, interval=limits, chi2values=chi2values, "pchisq", 1)
+	optRes <- optimize(lossFunctionLambdaKS, interval=limits, chi2values=chi2values, "pchisq", 1,df=df)
 	return(optRes$minimum)
 }
 chrom.char2num <- function(chrom) {

Modified: pkg/GenABEL/man/GenABEL.Rd
===================================================================
--- pkg/GenABEL/man/GenABEL.Rd	2012-10-06 11:27:18 UTC (rev 976)
+++ pkg/GenABEL/man/GenABEL.Rd	2012-10-11 10:41:09 UTC (rev 977)
@@ -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/estlambda.Rd
===================================================================
--- pkg/GenABEL/man/estlambda.Rd	2012-10-06 11:27:18 UTC (rev 976)
+++ pkg/GenABEL/man/estlambda.Rd	2012-10-11 10:41:09 UTC (rev 977)
@@ -3,12 +3,12 @@
 \title{Estimate the inflation factor for a distribution of P-values}
 \usage{
   estlambda(data, plot = FALSE, proportion = 1,
-    method = "regression", filter = TRUE, ...)
+    method = "regression", filter = TRUE, df = 1, ...)
 }
 \arguments{
   \item{data}{A vector of reals. If all are <=1, it is
   assumed that this is a vector of P-values, else it is
-  treated as a vector of chi-squares with 1 d.f.}
+  treated as a vector of chi-squares}
 
   \item{plot}{Wether the prot should be presented}
 
@@ -22,6 +22,8 @@
   chi-square should be excluded prior to estimation of
   Lambda}
 
+  \item{df}{Number of degrees of freedom}
+
   \item{...}{arguments passed to \code{\link{plot}}
   function}
 }