[Genabel-commits] r948 - pkg/GenABEL/R

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

Author: yurii
Date: 2012-08-30 11:26:00 +0200 (Thu, 30 Aug 2012)
New Revision: 948

Modified:
   pkg/GenABEL/R/qtscore.R
   pkg/GenABEL/R/reconstructNPs.R
   pkg/GenABEL/R/summary.snp.data.R
   pkg/GenABEL/R/summary.snp.data_old.R
Log:
fixing partial arguments match

Modified: pkg/GenABEL/R/qtscore.R
===================================================================
--- pkg/GenABEL/R/qtscore.R	2012-08-29 21:27:32 UTC (rev 947)
+++ pkg/GenABEL/R/qtscore.R	2012-08-30 09:26:00 UTC (rev 948)
@@ -254,7 +254,7 @@
 					lambda$se <- NA
 				} else {
 					if (lenn<100) warning("Number of observations < 100, Lambda estimate is unreliable")
-					lambda <- estlambda(chi2.1df,plot=FALSE,prop=propPs)
+					lambda <- estlambda(chi2.1df,plot=FALSE,proportion=propPs)
 					if (lambda$estimate<1.0 && clambda==TRUE) {
 						warning("Lambda estimated < 1, set to 1")
 						lambda$estimate <- 1.0
@@ -277,8 +277,8 @@
 			chi2.c1df <- chi2.1df/lambda$estimate
 			
 			if (is.logical(clambda)) {
-				lambda$iz0 <- estlambda(z0*z0,plot=FALSE,prop=propPs)$estimate 
-				lambda$iz2 <- estlambda(z2*z2,plot=FALSE,prop=propPs)$estimate
+				lambda$iz0 <- estlambda(z0*z0,plot=FALSE,proportion=propPs)$estimate 
+				lambda$iz2 <- estlambda(z2*z2,plot=FALSE,proportion=propPs)$estimate
 				if (clambda && lambda$iz0<1.0) {warning("z0 lambda < 1, set to 1");lambda$iz0<-1.0}
 				if (clambda && lambda$iz2<1.0) {warning("z2 lambda < 1, set to 1");lambda$iz2<-1.0}
 				chi2.c2df <- (z0*z0/lambda$iz0 + z2*z2/lambda$iz2 - 2.*z0*z2*rho/(sqrt(lambda$iz0*lambda$iz2)))/(1.- rho*rho)
@@ -331,8 +331,8 @@
 		#out$Pc2df <- pr.c2df/times
 		#out$Pc2df <- replace(out$Pc2df,(out$Pc2df==0),1/(1+times))
 	} else {
-		P1df <- pchisq(chi2.1df,1,lower=F)
-		P2df <- pchisq(chi2.2df,actdf,lower=F)
+		P1df <- pchisq(chi2.1df,1,lower.tail=F)
+		P2df <- pchisq(chi2.2df,actdf,lower.tail=F)
 		Pc1df <- NULL
 		#out$Pc1df <- pchisq(chi2.c1df,1,lower=F)
 		#out$Pc2df <- pchisq(chi2.c2df,2,lower=F)

Modified: pkg/GenABEL/R/reconstructNPs.R
===================================================================
--- pkg/GenABEL/R/reconstructNPs.R	2012-08-29 21:27:32 UTC (rev 947)
+++ pkg/GenABEL/R/reconstructNPs.R	2012-08-30 09:26:00 UTC (rev 948)
@@ -141,7 +141,7 @@
 	}
 # identify offspring and construct NPs
 	marIs.na <- function(matr,MAR) {
-		out <- apply(matr,MAR=MAR,FUN=function(x) {any(is.na(x))})
+		out <- apply(matr,MARGIN=MAR,FUN=function(x) {any(is.na(x))})
 		out
 	}
 	colIs.na <- function(matr) {return(marIs.na(matr,MAR=2))}

Modified: pkg/GenABEL/R/summary.snp.data.R
===================================================================
--- pkg/GenABEL/R/summary.snp.data.R	2012-08-29 21:27:32 UTC (rev 947)
+++ pkg/GenABEL/R/summary.snp.data.R	2012-08-30 09:26:00 UTC (rev 948)
@@ -48,7 +48,7 @@
 	
 	#dim(res) <- c(object at nsnps,9)
 	#res <- as.data.frame(res)
-	res[,9] <- pchisq(res[,9],1,lower=F)
+	res[,9] <- pchisq(res[,9],1,lower.tail=F)
 # X-chromosome
 	if (any(chromosome(object) == "X")) {
 		vec <- (chromosome(object) == "X")
@@ -66,7 +66,7 @@
 					as.integer(1),999)			
 			res[vec,7] <- resX[(nsnps(oX)*6+1):(nsnps(oX)*7)]
 			res[vec,8] <- resX[(nsnps(oX)*7+1):(nsnps(oX)*8)]
-			res[vec,9] <- pchisq(resX[(nsnps(oX)*8+1):(nsnps(oX)*9)],1,lower=F)
+			res[vec,9] <- pchisq(resX[(nsnps(oX)*8+1):(nsnps(oX)*9)],1,lower.tail=F)
 			rm(oX,vec,resX);gc(verbose=FALSE)
 		} else {
 			res[vec,7] <- rep(1,sum(vec))

Modified: pkg/GenABEL/R/summary.snp.data_old.R
===================================================================
--- pkg/GenABEL/R/summary.snp.data_old.R	2012-08-29 21:27:32 UTC (rev 947)
+++ pkg/GenABEL/R/summary.snp.data_old.R	2012-08-30 09:26:00 UTC (rev 948)
@@ -4,7 +4,7 @@
 		res <- .C("snp_summary_exhwe",as.raw(object at gtps),as.integer(object at nids),as.integer(object at nsnps), out = double(object at nsnps*9), PACKAGE="GenABEL")$out
 		dim(res) <- c(object at nsnps,9)
 		res <- as.data.frame(res)
-		res[,9] <- pchisq(res[,9],1,lower=F)
+		res[,9] <- pchisq(res[,9],1,lower.tail=F)
 # X-chromosome
 		if (any(object at chromosome == "X")) {
 		  vec <- (object at chromosome == "X")
@@ -13,7 +13,7 @@
 		    resX <- .C("snp_summary_exhwe",as.raw(oX at gtps),as.integer(oX at nids),as.integer(oX at nsnps), out = double(oX at nsnps*9), PACKAGE="GenABEL")$out
 		    res[vec,7] <- resX[(oX at nsnps*6+1):(oX at nsnps*7)]
 		    res[vec,8] <- resX[(oX at nsnps*7+1):(oX at nsnps*8)]
-		    res[vec,9] <- pchisq(resX[(oX at nsnps*8+1):(oX at nsnps*9)],1,lower=F)
+		    res[vec,9] <- pchisq(resX[(oX at nsnps*8+1):(oX at nsnps*9)],1,lower.tail=F)
 		    rm(oX,vec,resX);gc(verbose=FALSE)
 		  } else {
 		    res[vec,7] <- rep(1,sum(vec))