[Genabel-commits] r2084 - in pkg/MultiABEL: . R

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

Author: shenxia
Date: 2019-03-12 15:23:18 +0100 (Tue, 12 Mar 2019)
New Revision: 2084

Modified:
   pkg/MultiABEL/DESCRIPTION
   pkg/MultiABEL/NAMESPACE
   pkg/MultiABEL/R/MultiSecondary.R
   pkg/MultiABEL/R/MultiSummary.R
Log:
dependency and documentation bug fixed

Modified: pkg/MultiABEL/DESCRIPTION
===================================================================
--- pkg/MultiABEL/DESCRIPTION	2019-02-09 09:22:28 UTC (rev 2083)
+++ pkg/MultiABEL/DESCRIPTION	2019-03-12 14:23:18 UTC (rev 2084)
@@ -11,7 +11,8 @@
 Depends:
     R (>= 3.0),
     svMisc,
-    data.table
+    data.table,
+    mvtnorm
 Suggests:
     GenABEL,
     DatABEL

Modified: pkg/MultiABEL/NAMESPACE
===================================================================
--- pkg/MultiABEL/NAMESPACE	2019-02-09 09:22:28 UTC (rev 2083)
+++ pkg/MultiABEL/NAMESPACE	2019-03-12 14:23:18 UTC (rev 2084)
@@ -2,7 +2,7 @@
 importFrom("stats", "cor", "density", "lm", "na.omit", "pchisq", "pf",
              "qchisq", "qnorm", "quantile")
 importFrom("utils", "packageDescription", "read.table", "write.table")
-import("svMisc", "data.table")
-export("Multivariate", "MultiLoad","load.summary", "MultiSummary", "MultiSecondary", "MV.cor.test")
+import("svMisc", "data.table", "mvtnorm")
+export("Multivariate", "MultiLoad", "load.summary", "MultiSummary", "MultiSecondary", "MV.cor.test")
 exportClasses("multi.summary", "multi.loaded")
 useDynLib(MultiABEL, .registration = TRUE)
\ No newline at end of file

Modified: pkg/MultiABEL/R/MultiSecondary.R
===================================================================
--- pkg/MultiABEL/R/MultiSecondary.R	2019-02-09 09:22:28 UTC (rev 2083)
+++ pkg/MultiABEL/R/MultiSecondary.R	2019-03-12 14:23:18 UTC (rev 2084)
@@ -6,7 +6,7 @@
 #' @param LD.ref Regional LD matrix including SNPs in gwa.region
 #' @param snp.ref The reference alleles of SNPs in the reference LD correlation matrix. The names of the vector 
 #' should be SNP names in reference sample
-#' @param R.ref Shrinkage phenotypic correlation matrix, achieved from \code{MultiSummary()}
+#' @param R.ref Shrinkage phenotypic correlation matrix, achieved from \code{load.summary()}
 #' @param p.threshold P-value threshold in conditional analysis
 #' @param tol Tolerance for multicollinearity
 #' @param traits Traits to be analyzed

Modified: pkg/MultiABEL/R/MultiSummary.R
===================================================================
--- pkg/MultiABEL/R/MultiSummary.R	2019-02-09 09:22:28 UTC (rev 2083)
+++ pkg/MultiABEL/R/MultiSummary.R	2019-03-12 14:23:18 UTC (rev 2084)
@@ -119,7 +119,7 @@
 		mf <- mean(fs)
 		n.eff <- mf*2/(mf - 1) + m + 1 # effective N: fit a F-distribution to the observed fstat using moment estimator
 		res$n <- n 
-		res$effective.n <- round(n.eff, digits = 2)
+		# res$effective.n <- round(n.eff, digits = 2)
 		if (!high.dim) {
 			# if (n.eff < 5*m) {
 			#	warning('Effective sample size < 5 times number of phenotypes. Consider argument high.dim = TRUE.')
@@ -154,7 +154,7 @@
 		mf <- mean(fs)
 		n.eff <- mf*2/(mf - 1) + m + 1 # effective N: fit a F-distribution to the observed fstat using moment estimator
 		res$n <- n 
-		res$effective.n <- round(n.eff, digits = 2)
+		# res$effective.n <- round(n.eff, digits = 2)
 		if (!high.dim) {
 			# if (n.eff < 5*m) {
 			#	warning('Effective sample size < 5 times number of phenotypes. Consider argument high.dim = TRUE.')
@@ -189,7 +189,7 @@
 		mf <- mean(fs)
 		n.eff <- mf*2/(mf - 1) + m + 1 # effective N: fit a F-distribution to the observed fstat using moment estimator
 		res$n <- n 
-		res$effective.n <- round(n.eff, digits = 2)
+		# res$effective.n <- round(n.eff, digits = 2)
 		if (!high.dim) {
 			# if (n.eff < 5*m) {
 			#	warning('Effective sample size < 5 times number of phenotypes. Consider argument high.dim = TRUE.')
@@ -224,7 +224,7 @@
 		mf <- mean(fs)
 		n.eff <- mf*2/(mf - 1) + m + 1 # effective N: fit a F-distribution to the observed fstat using moment estimator
 		res$n <- n 
-		res$effective.n <- round(n.eff, digits = 2)
+		# res$effective.n <- round(n.eff, digits = 2)
 		if (!high.dim) {
 			# if (n.eff < 5*m) {
 			#	warning('Effective sample size < 5 times number of phenotypes. Consider argument high.dim = TRUE.')