myfuncs: loads a few functions I often need

#' A collection of utility functions
#' 
#' A collection of utility functions
#' 
#' 
#' @section Shortcuts:
#' \itemize{
#'   \item  \code{\link{catf}} and \code{\link{printf}} implement printf() like functions
#'   \item  \code{\link{os}} display memory usage
#'   \item  \link{shortcuts}: \code{l}, \code{h} and \code{p}: wrappers for \code{length}, \code{head} and \code{paste}
#'   \item  \code{\link{msd}} and \code{\link{ss}} mean and sd; sum of squares
#'   \item  \code{\link{zz}} save everything
#'   \item  \code{\link{myfuncs.reload}} reload the myfuncs package
#' }
#'
#' @section Graphics and plotting:
#' \itemize{
#'   \item  \code{\link{all.ablines}} Draw three lines (horizontal at 0, vertical at 0, and diagonal)
#'   \item  \code{\link{arrayplot}} Show image representation of a microarray
#'   \item  \code{\link{showgene}} beeswarm + boxplot for a gene 
#'   \item  \code{\link{myfaces}} My version of Chernoff faces
#'   \item  \code{\link{plotGenes}} Show expression for a number of genes in all arrays
#'   \item  \code{\link{dotpair}} A version of \code{pairs} showing also correlation coefficients
#'   \item  \code{\link{genePairs}} A version of \code{pairs} showing also correlation coefficients for large numbers of data points (using smoothScatter)
#'   \item  \code{\link{myPlotDensities}} A replacement for
#' \code{plotDensities} from \code{limma} for single-color arrays and for
#' coloring array groups
#'   \item  \code{\link{pairedswarm}} Beeswarm with lines linking pairs
#'   \item  \code{\link{clustCompPlot}} compare different clusterings in an overview plot
#'   \item  \code{\link{mypalette}} Nice color palette
#'   \item  \code{\link{pcaR2plot}} Calculate and visualize PCA regression
#'   \item  \code{\link{ttplot}} Plot a top table
#'   \item  \code{\link{copyan}} Produce an annotated PDF copy of a plot
#'}
#' @section Analysis:
#' \itemize{
#'   \item  \code{\link{getGOrilla}} run GOrilla from R
#'   \item  \code{\link{topTableAll}} produce a topTable-like output for all contrasts in a fit object
#'   \item  \code{\link{ttmake}} produce a topTable-like output including the msd measure
#'   \item  \code{\link{confuMat}} confusion matrix based on reality vs predictions

#' }
#' @section Data manipulation:
#' \itemize{
#'   \item  \code{\link{calcDif}} calculate pair differences in a limma object (for paired samples analysis)
#'   \item  \code{\link{grep.df}} Grep all columns of a data frame
#'   \item  \code{\link{repsapply}} general version of \code{avereps}
#' }
#' @section Others:
#' \itemize{
#'   \item  \code{\link{centers.predict}}
#'   \item  \code{\link{clustsizes}}
#'   \item  \code{\link{likelihood.test}}
#'   \item  \code{\link{lineq}}
#'   \item  \code{\link{matrixReshuffle}}
#'   \item  \code{\link{pca2var}}
#'   \item  \code{\link{pvals}}
#'   \item  \code{\link{rfvalid}}
#'   \item  \code{\link{ringfence}}
#'   \item  \code{\link{smoothPalette}}
#'   \item  \code{\link{twofacreshape}}
#' }
#' 
#'
#' @aliases myfuncs
#' @title My collection of utility functions
#' @name myfuncs-package
#' @docType package
#' @author January Weiner <january.weiner@@gmail.com>
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