fixed issues with documentation

Author: Peter Humburg

mePipe/DESCRIPTION

@@ -20,14 +20,3 @@ Imports:
     lmSupport
 Suggests:
     optparse
-Collate:
-    'covariates.R'
-    'options.R'
-    'plotHist.R'
-    'plotQQ.R'
-    'runME.R'
-    'ldStructure.R'
-    'utils.R'
-    'plotCov.R'
-    'multiPeaks.R'
-    'effectSize.R'

mePipe/NAMESPACE

@@ -1,3 +1,5 @@
+# Generated by roxygen2 (4.0.2): do not edit by hand
+
 export(allCovariates)
 export(chooseCov)
 export(covAssoc)

mePipe/R/covariates.R

@@ -164,8 +164,7 @@ loadCovariates <- function(files, options = getOptions()){
 }
 
 #' Combine two \code{SlicedData} objects
-#' @param x A \code{SlicedData} object
-#' @param y A \code{SlicedData} object
+#' @param ... \code{SlicedData} objects
 #' @return A \code{SlicedData} object containg the data from \code{x} and \code{y}
 #' 
 #' @author Peter Humburg

mePipe/R/effectSize.R

@@ -12,6 +12,7 @@
 #' @param exprOpt Options for reading of gene expression file. 
 #' @param genoOpt Options for reading of gene expression file.
 #' @param covOpt Options for reading of gene expression file.
+#' @param ... Further arguments (currently ignored).
 #' @return A \code{data.frame} similar to \code{hits} with two additional columns. Column
 #' \code{var.explained} gives the variance explained by the linear model that was fitted for 
 #' the SNP and column \code{effect.size} gives the variance explained by the genotype within

mePipe/R/multiPeaks.R

@@ -8,17 +8,19 @@
 #' @param hits \code{data.frame} with SNP-gene pairs and associsted p-value, 
 #' as produced by Matrix-eQTL. Additional columns may be included. In particular,
 #' output from \code{getLDpairs} is accepted.
-#' @param pvalue P-value threshold for association between secondary SNP and 
+#' @param p.value P-value threshold for association between secondary SNP and 
 #' gene expression.
 #' @param expression Gene expression data. This can either be the file name 
 #' or a \code{slicedData} object. 
 #' @param genotype Genotype data. This can either be the file name 
 #' or a \code{slicedData} object.
-#' @param covariat List of covariates to use. These can either be given as file names 
+#' @param covariate List of covariates to use. These can either be given as file names 
 #' or a \code{slicedData} objects.
 #' @param minFDR Minimum FDR for associations to be considered.
 #' @param minR Minimum R-squared at which two eSNPs will be assumed to have no independent 
 #' effect.
+#' @param snppos Name of file with SNP positions.
+#' @param window Window size around peak SNP.
 #' @param geneID If this argument is provided only associations with the given 
 #' gene are considered.
 #' @param exprOpt Options for reading of gene expression file. 
@@ -31,7 +33,7 @@
 #' @export
 getMultiPeak <- function(hits, p.value=1e-6, expression, genotype, covariate, minFDR,
 		minR, snppos, window, geneID, exprOpt=getOptions(), genoOpt=getOptions(), 
-		covOpt=getOptions(), output, ...){
+		covOpt=getOptions(), ...){
 	## only use peaks that reach significance
 	hits <- subset(hits, FDR <= minFDR)
 	if(!missing(geneID) && !is.null(geneID)) hits <- subset(hits, gene == geneID)

mePipe/R/runME.R

@@ -22,6 +22,8 @@
 #' @param verbose Flag indicating whether additional progress information should be printed.
 #' @param qqplot Flag indicating whether a QQ plot of p-values should be generated 
 #' rather than a histogram.
+#' @param cluster Logical indicating whether SGE jobs should be generated 
+#' instead of running locally.
 #' @return The object returned by \code{\link[MatrixEQTL]{Matrix_eQTL_main}}
 #' @note Before calling this function a call to \code{sge.setDefaultOptions} has to be made.
 #' @author Peter Humburg

mePipe/R/utils.R

@@ -87,7 +87,7 @@ loadData <- function(file, options){
 #' Obtain model summaries for Matrix-eQTL model 
 #' @param expression vector of expression values
 #' @param genotype vector of genotypes
-#' @param \code{data.frame} of covariates
+#' @param covariates \code{data.frame} of covariates
 #' @return A list as produced by \code{summary.lm} with additional entry \code{pr2} giving the partial
 #' r^2 for all effects in the model.
 #' 

mePipe/man/allCovariates.Rd

@@ -1,32 +1,28 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{allCovariates}
 \alias{allCovariates}
 \title{Run principle component analysis of gene expression data to generate
 table of possible covariates.}
 \usage{
-  allCovariates(expression, exprOpt = getOptions(), output,
-    sep = "\t")
+allCovariates(expression, exprOpt = getOptions(), output, sep = "\\t")
 }
 \arguments{
-  \item{expression}{Name of file containing the gene
-  expression data.}
+\item{expression}{Name of file containing the gene expression data.}
 
-  \item{exprOpt}{Options for reading of gene expression
-  data.}
+\item{exprOpt}{Options for reading of gene expression data.}
 
-  \item{output}{Name of file to which the principle
-  components should be saved (optional).}
+\item{output}{Name of file to which the principle components should be saved (optional).}
 
-  \item{sep}{Character used to separate entries in output
-  file.}
+\item{sep}{Character used to separate entries in output file.}
 }
 \value{
-  \code{data.frame} with all principle components
+\code{data.frame} with all principle components
 }
 \description{
-  Run principle component analysis of gene expression data
-  to generate table of possible covariates.
+Run principle component analysis of gene expression data to generate
+table of possible covariates.
 }
 \author{
-  Peter Humburg
+Peter Humburg
 }
 

mePipe/man/chooseCov.Rd

@@ -1,61 +1,51 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{chooseCov}
 \alias{chooseCov}
 \title{Determine the optimal number of covariates.}
 \usage{
-  chooseCov(expression, genotype, covariate,
-    candidates = seq(5, 50, by = 5), covThreshold = 0.01,
-    covOpt = getOptions(), output = "covSelect",
-    doCis = FALSE, doTrans = FALSE, ...)
+chooseCov(expression, genotype, covariate, candidates = seq(5, 50, by = 5),
+  covThreshold = 0.01, covOpt = getOptions(), output = "covSelect",
+  doCis = FALSE, doTrans = FALSE, ...)
 }
 \arguments{
-  \item{expression}{Name of file containing the gene
-  expression data.}
+\item{expression}{Name of file containing the gene expression data.}
 
-  \item{genotype}{Name of file containing the genotyping
-  data.}
+\item{genotype}{Name of file containing the genotyping data.}
 
-  \item{covariate}{Character vector of file names for
-  covariate files (see details).}
+\item{covariate}{Character vector of file names for covariate files (see details).}
 
-  \item{candidates}{Numeric vector listing the numbers of
-  covariates that should be evaluated.}
+\item{candidates}{Numeric vector listing the numbers of covariates that should be evaluated.}
 
-  \item{covThreshold}{FDR threshold to use when determining
-  the number of significant eQTLs.}
+\item{covThreshold}{FDR threshold to use when determining the number of significant eQTLs.}
 
-  \item{covOpt}{List of options to use for reading of
-  covariate data.}
+\item{covOpt}{List of options to use for reading of covariate data.}
 
-  \item{output}{Name of output directory}
+\item{output}{Name of output directory}
 
-  \item{doCis}{Logical indicating whether covariates should
-  be selected based on cis-associations.}
+\item{doCis}{Logical indicating whether covariates should be selected based on cis-associations.}
 
-  \item{doTrans}{Logical indicating whether covariates
-  should be selected based on trans-associations.}
+\item{doTrans}{Logical indicating whether covariates should be selected based on trans-associations.}
 
-  \item{...}{Addition parameters for \code{\link{runME}}}
+\item{...}{Addition parameters for \code{\link{runME}}}
 }
 \value{
-  A list with elements \item{covariates}{Numeric vector
-  with the number of covariates used in each iteration.}
-  \item{eqtls}{A list with components \code{significant}
-  and \code{all}. Each consisting of a numeric vector with
-  the number of genes that have significant associations or
-  any association with SNPs respectively.} \item{best}{Base
-  of file name(s) that contain the results of the run that
-  produced the most eQTLs.}
+A list with elements
+\item{covariates}{Numeric vector with the number of covariates used in each iteration.}
+\item{eqtls}{A list with components \code{significant} and \code{all}. Each consisting
+of a numeric vector with the number of genes that have significant associations or any
+association with SNPs respectively.}
+\item{best}{Base of file name(s) that contain the results of the run that produced the
+most eQTLs.}
 }
 \description{
-  Determine the optimal number of covariates.
+Determine the optimal number of covariates.
 }
 \details{
-  The argument \code{covariates} may be a vector of several
-  file names. In this case the first one will be used to
-  select varying numbers of covariates and the remaining
-  ones will always be used.
+The argument \code{covariates} may be a vector of several file names.
+In this case the first one will be used to select varying numbers of covariates and
+the remaining ones will always be used.
 }
 \author{
-  Peter Humburg
+Peter Humburg
 }
 

mePipe/man/combineSlicedData.Rd

@@ -1,22 +1,20 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{combineSlicedData}
 \alias{combineSlicedData}
 \title{Combine two \code{SlicedData} objects}
 \usage{
-  combineSlicedData(...)
+combineSlicedData(...)
 }
 \arguments{
-  \item{x}{A \code{SlicedData} object}
-
-  \item{y}{A \code{SlicedData} object}
+\item{...}{\code{SlicedData} objects}
 }
 \value{
-  A \code{SlicedData} object containg the data from
-  \code{x} and \code{y}
+A \code{SlicedData} object containg the data from \code{x} and \code{y}
 }
 \description{
-  Combine two \code{SlicedData} objects
+Combine two \code{SlicedData} objects
 }
 \author{
-  Peter Humburg
+Peter Humburg
 }