[Genabel-commits] r2054 - pkg/MultiABEL/man

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

Author: shenxia
Date: 2016-05-07 15:39:17 +0200 (Sat, 07 May 2016)
New Revision: 2054

Modified:
   pkg/MultiABEL/man/MultiSummary.Rd
   pkg/MultiABEL/man/Multivariate.Rd
   pkg/MultiABEL/man/load.summary.Rd
Log:


Modified: pkg/MultiABEL/man/MultiSummary.Rd
===================================================================
--- pkg/MultiABEL/man/MultiSummary.Rd	2016-05-07 13:24:56 UTC (rev 2053)
+++ pkg/MultiABEL/man/MultiSummary.Rd	2016-05-07 13:39:17 UTC (rev 2054)
@@ -6,7 +6,7 @@
 \alias{multi.summary}
 \title{Multivariate genome-wide association scan using summary statistics}
 \usage{
-MultiSummary(x, index = NULL, type = "outbred", vars = NULL)
+MultiSummary(x, index = NULL, type = "direct", vars = NULL)
 }
 \arguments{
 \item{x}{A data object of class \code{multi.summary} loaded by the function \code{load.summary}.}
@@ -62,14 +62,12 @@
 Xia Shen
 }
 \references{
-Xia Shen, Zheng Ning, Yakov Tsepilov, Masoud Shirali,  
-Generation Scotland, Blair H. Smith, Lynne J. Hocking, Sandosh Padmanabhan, Caroline Hayward, 
-David J. Porteous, Yudi Pawitan, Chris S. Haley, Yurii S. Aulchenko (2015).
-Simple multi-trait analysis identifies novel loci 
-associated with growth and obesity measures. \emph{Submitted}.
+Xia Shen, Zheng Ning, Yakov Tsepilov, Peter K. Joshi,
+James F. Wilson, Yudi Pawitan, Chris S. Haley, Yurii S. Aulchenko (2016).
+Fast pleiotropic meta-analysis for genetic studies. \emph{Submitted}.
 }
 \seealso{
-\code{load.summary}, \code{Multivariate}
+\code{load.summary}
 }
 \keyword{meta-analysis}
 \keyword{multivariate,}

Modified: pkg/MultiABEL/man/Multivariate.Rd
===================================================================
--- pkg/MultiABEL/man/Multivariate.Rd	2016-05-07 13:24:56 UTC (rev 2053)
+++ pkg/MultiABEL/man/Multivariate.Rd	2016-05-07 13:39:17 UTC (rev 2054)
@@ -50,7 +50,7 @@
 Xia Shen
 }
 \references{
-Xia Shen, ..., Gordan Lauc, Jim Wilson, Yurii Aulchenko (2015).
+Xia Shen, ..., Jim Wilson, Gordan Lauc, Yurii Aulchenko (2015).
 Multi-omic-variate analysis identified novel loci associated with 
 compound N-Glycosylation of human Immunoglobulin G. \emph{Submitted}.
 }

Modified: pkg/MultiABEL/man/load.summary.Rd
===================================================================
--- pkg/MultiABEL/man/load.summary.Rd	2016-05-07 13:24:56 UTC (rev 2053)
+++ pkg/MultiABEL/man/load.summary.Rd	2016-05-07 13:39:17 UTC (rev 2054)
@@ -5,8 +5,7 @@
 \title{Loading multiple summary statistics from genome-wide association studies}
 \usage{
 load.summary(files, cor.pheno = NULL, indep.snps = NULL, est.var = FALSE,
-  type = "outbred", vars = NULL, columnNames = c("snp", "a1", "freq",
-  "beta", "se", "n"), fixedN = NULL)
+  columnNames = c("snp", "a1", "freq", "beta", "se", "n"), fixedN = NULL)
 }
 \arguments{
 \item{files}{A vector of file names as strings. Each file name should contain summary statistics of
@@ -30,24 +29,17 @@
 If \code{TRUE}, each phenotypic variance will be estimated to adjust the summary statistics, so that
 the corresponding phenoypic variance is 1.}
 
-\item{type}{A string gives the type of analysis. Default is \code{"outbred"}, referring to 
-general outbred populations, following Hardy-Weinberg equilibrium. \code{"inbred"} refers to 
-inbred populations, where no heterzygotes exists, namely, allele frequency = genotype frequency.
-\code{"precise"} refers to precise genotypic variance, especially when the individual-level data 
-are available, for which the argument \code{vars} has to be given.}
-
-\item{vars}{A numeric vector gives the variance of the genotypes at each SNP, e.g. coded as 0, 1 and 2.
-Only used when \code{type = "precise"}.}
-
 \item{columnNames}{A vector with names of columns containing necessary information in the input file;
-default values are c('snp','a1','freq','beta','se','n'). The values are case-insensitive.}
+default values are c('snp','a1','freq','beta','se','n'). The values are case-insensitive. Note: check
+your allele definitions for different traits are based on the same strand!}
 
 \item{fixedN}{sample size to assume across all analyses, when provided, this number will be used
 (instead of the ones specified in the input files)}
 }
 \value{
 The function returns a list of class \code{multi.summary}, containing two elements: \code{gwa}
-(the cleaned data to be processed in multi-trait GWAS) and \code{cor.pheno} (user input or estimated).
+(the cleaned data to be processed in multi-trait GWAS), \code{cor.pheno} (user input or estimated), and 
+\code{var.pheno} (default or estimated).
 }
 \description{
 The function loads multiple meta-GWAS summary statistics, for subsequent multi-trait GWAS. 
@@ -76,7 +68,7 @@
 }
 }
 \author{
-Xia Shen, Yurii Aulchenko
+Xia Shen, Yurii S. Aulchenko
 }
 \references{
 Xia Shen, Zheng Ning, Yakov Tsepilov, Masoud Shirali,