[Genabel-commits] r1563 - pkg/MetABEL/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jan 26 23:02:29 CET 2014
Author: lckarssen
Date: 2014-01-26 23:02:28 +0100 (Sun, 26 Jan 2014)
New Revision: 1563
Modified:
pkg/MetABEL/man/forestplot.Rd
pkg/MetABEL/man/metagwa.files.Rd
pkg/MetABEL/man/metagwa.tables.Rd
Log:
Fixes and small corrections in the MetABEL documentation.
This fixes several NOTEs when checking with --as-cran (lines that were too long).
Also fixes some spelling or upper/lower case bugs and contains some code layout improvements.
Modified: pkg/MetABEL/man/forestplot.Rd
===================================================================
--- pkg/MetABEL/man/forestplot.Rd 2014-01-26 21:49:46 UTC (rev 1562)
+++ pkg/MetABEL/man/forestplot.Rd 2014-01-26 22:02:28 UTC (rev 1563)
@@ -4,30 +4,34 @@
\description{
Function to draw meta-analysis forest plots
}
+
\usage{
-forestplot(estimate, se, labels = paste("Study", c(1:length(estimate))), CI = 0.95, xexp = FALSE, ...)
+ forestplot(estimate, se, labels = paste("Study", c(1:length(estimate))),
+ CI = 0.95, xexp = FALSE, ...)
}
+
\arguments{
- \item{estimate}{vector of effect estimates}
- \item{se}{vector of standard errors}
- \item{labels}{individual study labels}
- \item{CI}{confidence interval, e.g. 0.95}
- \item{xexp}{whether the effect values are to be depicted on exponential scale}
- \item{\dots}{arguments passed to plot function, e.g. main = "My plot"}
+ \item{estimate}{Vector of effect estimates}
+ \item{se}{Vector of standard errors}
+ \item{labels}{Individual study labels}
+ \item{CI}{Confidence interval, e.g. 0.95}
+ \item{xexp}{Whether the effect values are to be depicted on exponential scale}
+ \item{\dots}{Arguments passed to plot function, e.g. main = "My plot"}
}
+
%\details{
%}
%\value{
%}
%\references{ ~put references to the literature/web site here ~ }
\author{Yurii Aulchenko}
-%\note{ ~~further notes~~
+%\note{ ~~further notes~~
%}
%\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
\examples{
-beta <- c(0.16,0.091,0.072,-0.03)
-s <- c(0.07,0.042,0.048,0.12)
-forestplot(beta,s,main="Example plot")
+ beta <- c(0.16, 0.091, 0.072, -0.03)
+ se <- c(0.07, 0.042, 0.048, 0.12)
+ forestplot(beta, se, main="Example plot")
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
Modified: pkg/MetABEL/man/metagwa.files.Rd
===================================================================
--- pkg/MetABEL/man/metagwa.files.Rd 2014-01-26 21:49:46 UTC (rev 1562)
+++ pkg/MetABEL/man/metagwa.files.Rd 2014-01-26 22:02:28 UTC (rev 1563)
@@ -5,47 +5,53 @@
Performes meta-analysis of results of multiple GWA studies
stored in files.
}
+
\usage{
-metagwa.files(dir = ".", pops, extens, maf = 5, call = 0.95, phwe = 1e-08, precorrect=TRUE, correct.pooled = FALSE)
+ metagwa.files(dir = ".", pops, extens, maf = 5, call = 0.95, phwe = 1e-08,
+ precorrect=TRUE, correct.pooled = FALSE)
}
\arguments{
- \item{dir}{path to directory containing files with GWA results}
- \item{pops}{A vector specifying study names, which make the first
- part of the file names}
- \item{extens}{fixed extension to the file name}
- \item{maf}{filter threshold for the absolute number/frequency of minor allele.
- If the parameter is < 1, this MAF threshold is used for filtering before
- meta-analysis; if this parameter is >1, n*MAF -- absolute number of
- the minor allele copies -- is used}
- \item{call}{filter threshold for SNP call rate}
- \item{phwe}{filter threshold for SNP P-value for HWE}
+ \item{dir}{Path to directory containing files with GWA results}
+ \item{pops}{A vector specifying study names, which make the first
+ part of the file names}
+ \item{extens}{Fixed extension to the file name}
+ \item{maf}{Filter threshold for the absolute number/frequency of minor allele.
+ If the parameter is < 1, this MAF threshold is used for filtering before
+ meta-analysis; if this parameter is >1, n*MAF -- absolute number of
+ the minor allele copies -- is used}
+ \item{call}{Filter threshold for SNP call rate}
+ \item{phwe}{Filter threshold for SNP P-value for HWE}
\item{precorrect}{Should GC be applied to the original data before pooling}
- \item{correct.pooled}{Whether to apply Genomic Control correction to the study named "POOLED"}
+ \item{correct.pooled}{Whether to apply Genomic Control correction to
+ the study named "POOLED"}
}
+
\details{
- Th function looks for files named "POPSextens" in the directory "dir", reads them
- and pool consecutively using \code{\link{metagwa.tables}} function.
+ The function looks for files named "POPSextens" in the directory
+ "dir", reads them and pool consecutively using
+ \code{\link{metagwa.tables}} function.
- The source files should contain a number of variables, such as allelic coding,
- code for the effective allele, etc. Please refer to formetascore function
- of GenABEL package for details.
+ The source files should contain a number of variables, such as allelic
+ coding, code for the effective allele, etc. Please refer to the
+ formetascore function of GenABEL package for details.
- When the file is not available for the first population, or there are non-unique
- population names, the function stops with an error message.
+ When the file is not available for the first population, or there are
+ non-unique population names, the function stops with an error message.
- If there are no files corresponding to next populations, these are skipped
- in analysis with a warning message (see details in the description of returned
- values).
+ If there are no files corresponding to next populations, these are
+ skipped in analysis with a warning message (see details in the
+ description of returned values).
}
+
\value{
- Results are dumped to file named "POOLEDextens" in the directory "dir".
-
- Additionally, a list is returned with elements
- \item{analysed.pops}{list of populations successfully analysed}
+ Results are dumped to file named "POOLEDextens" in the directory
+ "dir". Additionally, a list is returned with elements
+ \item{analysed.pops}{list of populations successfully analysed}
}
+
%\references{ ~put references to the literature/web site here ~ }
\author{Yurii Aulchenko}
-%\note{ ~~further notes~~
+%\note{ ~~further notes~~
%}
\seealso{\code{\link{metagwa.tables}}}
%\examples{
Modified: pkg/MetABEL/man/metagwa.tables.Rd
===================================================================
--- pkg/MetABEL/man/metagwa.tables.Rd 2014-01-26 21:49:46 UTC (rev 1562)
+++ pkg/MetABEL/man/metagwa.tables.Rd 2014-01-26 22:02:28 UTC (rev 1563)
@@ -4,8 +4,10 @@
\description{
Performes meta-analysis of results of two individual GWA studies
}
+
\usage{
-metagwa.tables(data.x, data.y, name.x = "P1", name.y = "P2", precorrect=TRUE, correct.pooled = FALSE)
+ metagwa.tables(data.x, data.y, name.x = "P1", name.y = "P2",
+ precorrect=TRUE, correct.pooled = FALSE)
}
\arguments{
\item{data.x}{First data frame with GWA data}
@@ -13,17 +15,22 @@
\item{name.x}{First study name}
\item{name.y}{Second study name}
\item{precorrect}{Should GC be applied to the original data before pooling}
- \item{correct.pooled}{Whether to apply Genomic Control correction to the study named "POOLED"}
+ \item{correct.pooled}{Whether to apply Genomic Control correction to
+ the study named "POOLED"}
}
+
\details{
- Original data frames should contain a number of variables, such as allelic coding,
- code for the effective allele, etc. Please refer to formetascore function
- of GenABEL package for details.
+ Original data frames should contain a number of variables,
+ such as allelic coding, code for the effective allele,
+ etc. Please refer to formetascore function of GenABEL package
+ for details.
}
+
\value{
- A data frame containing summary statistics and essential details of the individual
- studies
+ A data frame containing summary statistics and essential details
+ of the individual studies
}
+
%\references{}
\author{Yurii Aulchenko}
%\note{}
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