[Genabel-commits] r2061 - in pkg/MultiABEL: . R

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

Author: shenxia
Date: 2016-12-24 11:54:02 +0100 (Sat, 24 Dec 2016)
New Revision: 2061

Modified:
   pkg/MultiABEL/ChangeLog
   pkg/MultiABEL/R/MultiSummary.R
Log:
MultiSummary() NaN bug fixed when index is specified.

Modified: pkg/MultiABEL/ChangeLog
===================================================================
--- pkg/MultiABEL/ChangeLog	2016-12-16 13:55:23 UTC (rev 2060)
+++ pkg/MultiABEL/ChangeLog	2016-12-24 10:54:02 UTC (rev 2061)
@@ -1,3 +1,8 @@
+2016-12-24 18:09 xia
+
+    * MultiSummary() NaN bug fixed when index 
+      is specified.
+
 2016-05-07 14:16 xia
 
     * Updated to version 1.1-5

Modified: pkg/MultiABEL/R/MultiSummary.R
===================================================================
--- pkg/MultiABEL/R/MultiSummary.R	2016-12-16 13:55:23 UTC (rev 2060)
+++ pkg/MultiABEL/R/MultiSummary.R	2016-12-24 10:54:02 UTC (rev 2061)
@@ -61,9 +61,10 @@
 		stop('Wrong data type!')
 	}
 	cat('Multi-trait genome scan ... ')
-	if (!is.null(index)) {
+	if (!is.null(index) & length(index) < nrow(x$cor.pheno)) {
 		m <- nrow(x$cor.pheno)
 		x$cor.pheno <- x$cor.pheno[index,index]
+		x$var.pheno <- x$var.pheno[index]
 		idx <- which(!(1:m %in% index))
 		x$gwa <- x$gwa[,-c(idx*2 - 1, idx*2)]
 	}
@@ -84,7 +85,7 @@
 	}
 	dimnames(betamat) <- list(NULL, NULL)
 	res <- data.frame(marker = rownames(x$gwa), freq = f, n = n,
-		stringsAsFactors=FALSE)
+		stringsAsFactors = FALSE)
 	rownames(res) <- rownames(x$gwa)
 	if (type != 'direct') {
 		bnames <- paste0('beta.cond.', rownames(x$cor.pheno))