[Genabel-commits] r1793 - pkg/MixABEL/R

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

Author: lckarssen
Date: 2014-08-10 17:29:11 +0200 (Sun, 10 Aug 2014)
New Revision: 1793

Modified:
   pkg/MixABEL/R/fgls.R
Log:
Fixed a few partial arguments in MixABEL's fgls.R code (found by R CMD check).


Modified: pkg/MixABEL/R/fgls.R
===================================================================
--- pkg/MixABEL/R/fgls.R	2014-08-10 15:25:14 UTC (rev 1792)
+++ pkg/MixABEL/R/fgls.R	2014-08-10 15:29:11 UTC (rev 1793)
@@ -112,7 +112,7 @@
         rownames(betaW) <- colnames(X)
         dimnames(V) <- list(colnames(X),colnames(X))
         out <- list(beta=betaW,V=V,T2=T2,df=sum(whichtest),tested=whichtest,
-                        meanColX = apply(X,FUN=mean,MAR=2), n = dim(X)[1])
+                        meanColX = apply(X,FUN=mean,MARGIN=2), n = dim(X)[1])
         class(out) <- "FGLS"
         out
 }
@@ -134,7 +134,7 @@
 #' @author Yurii Aulchenko
 #'
 summaryFGLS <- function(x,verbosity=1,varcov=FALSE,include.means=FALSE) {
-        out <- c(x$n,x$T2,x$df,pchisq(x$T2,df=x$df,low=FALSE))
+        out <- c(x$n,x$T2,x$df,pchisq(x$T2,df=x$df,lower.tail=FALSE))
         names(out) <- c("n","Chisq","df","P-value")
         if (verbosity == 0) {
                 return(out)
@@ -435,7 +435,7 @@
 
                                 if (nocalls > 0) {
                                         if (na.SNP=="impute") {
-                                                mn <- apply(GGG,MAR=2,FUN=mean,na.rm=TRUE)
+                                                mn <- apply(GGG,MARGIN=2,FUN=mean,na.rm=TRUE)
                                                 for (iii in 1:dim(GGG)[2]) GGG[is.na(GGG[,iii]),iii] <- mn[iii]
                                         } else if (na.SNP == "drop") {
                                                 #stop("na.SNP != 'impute' and nocalls > 0; 'drop' not yet implemented")
@@ -546,7 +546,7 @@
                 vcoSeq <- as.vector(tmpMtr[lower.tri(tmpMtr)])
                 #print("before cbind")
                 out$FGLS <- cbind(outN,resIteratorNew[,1,drop=FALSE],
-                                outdf,pchisq(resIteratorNew[,1,drop=FALSE],df=outdf,low=FALSE),
+                                outdf,pchisq(resIteratorNew[,1,drop=FALSE],df=outdf,lower.tail=FALSE),
                                 resIteratorNew[,c(2:(1+nBeta)),drop=FALSE],
                                 sqrt(resIteratorNew[,c((1+nBeta)+varSeq),drop=FALSE]),
                                 resIteratorNew[,c((rIsize-nBeta+1):rIsize),drop=FALSE],