[Genabel-commits] r2079 - pkg/MultiABEL/man

Sat Feb 9 04:33:00 CET 2019

Author: shenxia
Date: 2019-02-09 04:33:00 +0100 (Sat, 09 Feb 2019)
New Revision: 2079

Modified:
   pkg/MultiABEL/man/MultiABEL.Rd
   pkg/MultiABEL/man/MultiLoad.Rd
   pkg/MultiABEL/man/MultiRep.Rd
   pkg/MultiABEL/man/MultiSummary.Rd
   pkg/MultiABEL/man/Multivariate.Rd
   pkg/MultiABEL/man/load.summary.Rd
Log:
update manuals

Modified: pkg/MultiABEL/man/MultiABEL.Rd
===================================================================

--- pkg/MultiABEL/man/MultiABEL.Rd	2019-02-09 03:32:22 UTC (rev 2078)
+++ pkg/MultiABEL/man/MultiABEL.Rd	2019-02-09 03:33:00 UTC (rev 2079)
@@ -5,7 +5,6 @@
 \alias{MultiABEL}
 \alias{multiabel}
 \alias{MultiABEL-package}
-\alias{MultiABEL-package}
 \title{Multivariate GWAS in R}
 \description{
 MultiABEL: Multivariate Genome-Wide Association Analyses

Modified: pkg/MultiABEL/man/MultiLoad.Rd
===================================================================
--- pkg/MultiABEL/man/MultiLoad.Rd	2019-02-09 03:32:22 UTC (rev 2078)
+++ pkg/MultiABEL/man/MultiLoad.Rd	2019-02-09 03:33:00 UTC (rev 2079)
@@ -6,9 +6,9 @@
 \alias{multiload}
 \title{Load individual-level data for multivariate GWA analysis}
 \usage{
-MultiLoad(gwaa.data = NULL, phenofile = NULL, genofile = NULL, trait.cols,
-  covariate.cols = NULL, cuts = 20, impute = TRUE, gaussianize = TRUE,
-  ...)
+MultiLoad(gwaa.data = NULL, phenofile = NULL, genofile = NULL,
+  trait.cols, covariate.cols = NULL, cuts = 20, impute = TRUE,
+  gaussianize = TRUE, ...)
 }
 \arguments{
 \item{gwaa.data}{An (optional) object of \code{{gwaa.data-class}}.}

Modified: pkg/MultiABEL/man/MultiRep.Rd
===================================================================
--- pkg/MultiABEL/man/MultiRep.Rd	2019-02-09 03:32:22 UTC (rev 2078)
+++ pkg/MultiABEL/man/MultiRep.Rd	2019-02-09 03:33:00 UTC (rev 2079)
@@ -76,9 +76,12 @@
 }
 }
 \references{
-Xia Shen, ..., Gordan Lauc, Jim Wilson, Yurii Aulchenko (2014).
-Multi-omic-variate analysis identified the association between 14q32.33 and 
-compound N-Glycosylation of human Immunoglobulin G \emph{Submitted}.
+Shen X, Klaric L, Sharapov S, Mangino M, Ning Z, Wu D, 
+Trbojevic-Akmacic I, Pucic-Bakovic M, Rudan I, Polasek O, 
+Hayward C, Spector TD, Wilson JF, Lauc G, Aulchenko YS (2017): 
+Multivariate discovery and replication of five novel loci 
+associated with Immunoglobulin G N-glycosylation. 
+\emph{Nature Communications}, 8, 447; doi: 10.1038/s41467-017-00453-3.
 }
 \seealso{
 \code{\link{Multivariate}}

Modified: pkg/MultiABEL/man/MultiSummary.Rd
===================================================================
--- pkg/MultiABEL/man/MultiSummary.Rd	2019-02-09 03:32:22 UTC (rev 2078)
+++ pkg/MultiABEL/man/MultiSummary.Rd	2019-02-09 03:33:00 UTC (rev 2079)
@@ -6,7 +6,8 @@
 \alias{multi.summary}
 \title{Multivariate genome-wide association scan using summary statistics}
 \usage{
-MultiSummary(x, index = NULL, type = "direct", vars = NULL)
+MultiSummary(x, index = NULL, type = "direct", vars = NULL,
+  high.dim = FALSE)
 }
 \arguments{
 \item{x}{A data object of class \code{multi.summary} loaded by the function \code{load.summary}.}
@@ -23,11 +24,15 @@
 
 \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{high.dim}{Are the phenotypes high-dimensional or not? This is particularly important when the ratio
+of the number of individuals (n) to the number of phenotypes being analyzed (p) is not big enough, e.g when
+analyzing a big number of omics phenotypes in a small cohort. Default = \code{FALSE}.}
 }
 \value{
 The function returns a data frame containing the multi-trait GWAS results, where the row names are
 the variants names. The column names are: variant name (\code{Marker}), allele frequency (\code{Freq}),
-the smallest sample size of the traits (\code{N}), effect on the phenotype score (\code{Beta.S}, see reference),
+the effective sample size of the multiple traits (\code{N}), effect on the phenotype score (\code{Beta.S}, see reference),
 standard error (\code{SE}), p-value (\code{P}), and the rest the coefficients to construct the phenotype score
 (see reference).
 }
@@ -59,9 +64,11 @@
 }
 }
 \references{
-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}.
+Zheng Ning, Yakov Tsepilov, Peter K. Joshi,
+James F. Wilson, Yudi Pawitan, Chris S. Haley, 
+Yurii S. Aulchenko, Xia Shen (2018).
+Pleiotropic meta-analysis for genomic studies: discovery, replication, 
+and interpretation. \emph{Submitted}.
 }
 \seealso{
 \code{load.summary}

Modified: pkg/MultiABEL/man/Multivariate.Rd
===================================================================
--- pkg/MultiABEL/man/Multivariate.Rd	2019-02-09 03:32:22 UTC (rev 2078)
+++ pkg/MultiABEL/man/Multivariate.Rd	2019-02-09 03:33:00 UTC (rev 2079)
@@ -48,9 +48,12 @@
 
 }
 \references{
-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}.
+Shen X, Klaric L, Sharapov S, Mangino M, Ning Z, Wu D, 
+Trbojevic-Akmacic I, Pucic-Bakovic M, Rudan I, Polasek O, 
+Hayward C, Spector TD, Wilson JF, Lauc G, Aulchenko YS (2017): 
+Multivariate discovery and replication of five novel loci 
+associated with Immunoglobulin G N-glycosylation. 
+\emph{Nature Communications}, 8, 447; doi: 10.1038/s41467-017-00453-3.
 }
 \seealso{
 \code{\link{MultiLoad}}

Modified: pkg/MultiABEL/man/load.summary.Rd
===================================================================
--- pkg/MultiABEL/man/load.summary.Rd	2019-02-09 03:32:22 UTC (rev 2078)
+++ pkg/MultiABEL/man/load.summary.Rd	2019-02-09 03:33:00 UTC (rev 2079)
@@ -4,9 +4,9 @@
 \alias{load.summary}
 \title{Loading multiple summary statistics from genome-wide association studies}
 \usage{
-load.summary(files, cor.pheno = NULL, indep.snps = NULL, est.var = FALSE,
-  columnNames = c("snp", "a1", "a2", "freq", "beta", "se", "n"),
-  fixedN = NULL)
+load.summary(files, cor.pheno = NULL, indep.snps = NULL,
+  est.var = FALSE, columnNames = c("snp", "a1", "a2", "freq", "beta",
+  "se", "n"), fixedN = NULL, data.table = TRUE)
 }
 \arguments{
 \item{files}{A vector of file names as strings. Each file name should contain summary statistics of

