single install.R for windows/linux

[cpanse]

#R

# Christian Panse <cp@fgcz.ethz.ch>
# Functional Genomics Center Zurich 2018

# System Requirements
pkgs <- c( 'devtools',
  'dplyr',
  'ggplot2',
  'hexbin',
  'magrittr',
  'parallel',
  'protViz',
  'rmarkdown',
  'RSQLite',
  'scales',
  'shiny',
  'tidyr',
  'tidyverse',
  'DT')

(pkgs <- pkgs[(!pkgs %in% unique(installed.packages()[,'Package']))])
if(length(pkgs) > 0){install.packages(pkgs)}

# Installation
install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawDiag_0.0.28.tar.gz', repos=NULL)

# Testing
library(rawDiag)
(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))
system.time(RAW <- read.raw(file = rawfile))
dim(RAW)
summary.rawDiag(RAW)
PlotScanFrequency(RAW)

# read all dimensions
dim(RAW)
RAW <- read.raw(file = rawfile, rawDiag = FALSE)
dim(RAW)

R.version.string; Sys.info()[c('sysname', 'version')]

run the rawDiag shiny application

library(rawDiag)

# root defines where your raw files are
rawDiagShiny(root="D:/Data2San/")

run as BAT script on the windows box

"c:\Program Files\R\R-3.5.1\bin\R.exe" -e "library(rawDiag); rawDiagShiny(root='D:/Data2San', launch.browser=TRUE)"

or from the Linux/Apple command line

R -e "library(rawDiag); rawDiagShiny(root='$HOME/Downloads', launch.browser=TRUE)"

and you can add it to you $HOME/.bashrc

alias rawDiag="R -e \"library(rawDiag); rawDiagShiny(root='$HOME/Downloads', launch.browser=TRUE)\""

[jjGG]

hei, works on my mac without a problem. Only for XIC extraction (if I click "extract main peak") I get the error.. ///////// console /////// displays XICs of given masses. arguments imply differing number of rows: 50, 0

[jjGG]

Reopened on request of CP ;)