Initial commit after the meetup

Author: xrobin

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData

DESCRIPTION

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+Package: xavamess
+Type: Package
+Title: Various useful functions
+Version: 0.1
+Date: 2015-02-05
+Author: Xavier Robin
+Maintainer: Xavier Robin <[email protected]>
+Description: This package contains one useful function
+License: GPL-3
+Imports: stringr

NAMESPACE

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+# Generated by roxygen2 (4.1.0): do not edit by hand
+
+export(elongate)
+importFrom(stringr,str_split)

R/elongate.R

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+#' @title Elongates a pseudo-wide column
+#' @description Takes a pseudo-wide column and tranform it into a long format
+#' @param id a column that will not be splitted
+#' @param wide the column to split
+#' @param pattern the character or regex used to split up the wide column (see \link{str_split})
+#' @examples 
+#' data(pseudo.wide)
+#' elongated.score <- elongate(pseudo.wide$Protein, pseudo.wide$Score)
+#' elongated.sequence <- elongate(pseudo.wide$Protein, pseudo.wide$Sequence)
+#' # The following works only if the Score and Sequence have the same pattern
+#' # (ie same number of splits per ID)
+#' elongated <- data.frame(Protein = elongated.score$id, 
+#'                         Score = elongated.score$wide,
+#'                         Sequence = elongated.sequence$wide)
+#' \dontshow{
+#' stopifnot(identical(dim(elongated.score), dim(elongated.sequence)))
+#' }
+#' @importFrom stringr str_split
+#' @export
+elongate <- function(id, wide, pattern = ";") {
+  splitted <- str_split(wide, pattern)
+  long <- data.frame(id = rep.int(id, sapply(splitted, length)), wide = unlist(splitted))
+  return(long)
+}
+
+
+

R/pseudo.wide.R

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+#' A dummy data set in pseudo-wide format
+#' @docType data
+#' @name pseudo.wide
+#' @description This data set list proteins with two pseudo-wide columns
+#' containing the identified sequence and associate score
+#' @format a \code{data.frame} with 3 columns.
+NULL

data/pseudo.wide.RData

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+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/elongate.R
+\name{elongate}
+\alias{elongate}
+\title{Elongates a pseudo-wide column}
+\usage{
+elongate(id, wide, pattern = ";")
+}
+\arguments{
+\item{id}{a column that will not be splitted}
+
+\item{wide}{the column to split}
+
+\item{pattern}{the character or regex used to split up the wide column (see \link{str_split})}
+}
+\description{
+Takes a pseudo-wide column and tranform it into a long format
+}
+\examples{
+data(pseudo.wide)
+elongated.score <- elongate(pseudo.wide$Protein, pseudo.wide$Score)
+elongated.sequence <- elongate(pseudo.wide$Protein, pseudo.wide$Sequence)
+# The following works only if the Score and Sequence have the same pattern
+# (ie same number of splits per ID)
+elongated <- data.frame(Protein = elongated.score$id,
+                        Score = elongated.score$wide,
+                        Sequence = elongated.sequence$wide)
+\dontshow{
+stopifnot(identical(dim(elongated.score), dim(elongated.sequence)))
+}
+}
+

man/elongate.Rd

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+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/pseudo.wide.R
+\docType{data}
+\name{pseudo.wide}
+\alias{pseudo.wide}
+\title{A dummy data set in pseudo-wide format}
+\format{a \code{data.frame} with 3 columns.}
+\description{
+This data set list proteins with two pseudo-wide columns
+containing the identified sequence and associate score
+}
+

man/pseudo.wide.Rd

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+\name{xavamess-package}
+\alias{xavamess-package}
+\alias{xavamess}
+\docType{package}
+\title{
+Various useful functions
+}
+\description{
+This package contains one useful function
+}
+\details{
+\tabular{ll}{
+Package: \tab xavamess\cr
+Type: \tab Package\cr
+Version: \tab 0.1\cr
+Date: \tab 2015-02-05\cr
+License: \tab GPL-3\cr
+}
+}
+\author{
+Xavier Robin
+
+Maintainer: Xavier Robin <xavier.robin@bric.ku.dk>
+}
+%\references{
+%~~ Literature or other references for background information ~~
+%}
+\keyword{ package }
+%\seealso{
+%~~ Optional links to other man pages, e.g. ~~
+%~~ \code{\link[<pkg>:<pkg>-package]{<pkg>}} ~~
+%}