ABRF R4Core

rawDiag version 0.0.41

Install

1. System Requirements

a Windows/Linux/MacOSX x64 platform

1.1 .NET Framework and R

• https://www.mono-project.com/ (>4.0.22) for (Linux and MacOSX)
• .NET Framework 4.5.1 or higher (Windows)
• R (>4.0);
• U.S. language setting on windows/linux/apple see issue 33

You can download and install the current R package.

run R (>= 4.0) and type

# install required packages 
pkgs <- c('dplyr', 'hexbin', 'protViz', 'RSQLite', 'scales', 'tidyr', 'tidyverse', 'shiny')
pkgs <- pkgs[(!pkgs %in% unique(installed.packages()[,'Package']))]
if(length(pkgs) > 0){install.packages(pkgs)}

install rawDiag

install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawDiag_0.0.41.tar.gz', repo=NULL)

it should run out of the box. A possible first code snippet is below

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

After Install please send us an Email, SUBJECT rawDiag package.

What kind of instrument data do you use?

If you still have problems, please let us know via Email, SUBJECT request help rawDiag package.

Output of R's function sessionInfo()

New features

0. removed data used in our initial JPR publication (slim)

1. refactored read.raw.info

2. some code cosmetics for depreciated dplyr methods

slim

rawDiag version 0.0.38

Thank you for your interest in the rawDiag package.

please use the build package.

If you accept the Thermo License agreement

https://github.com/fgcz/rawDiag/blob/master/inst/docker/ThermoRawFileReader/RawFileReaderLicense.doc

Install

1. System Requirements

a Windows/Linux/MacOSX x64 platform

1.1 .NET Framework and R

• https://www.mono-project.com/ (>4.0.22) for (Linux and MacOSX)
• .NET Framework 4.5.1 or higher (Windows)
• R (>4.0);
• U.S. language setting on windows/linux/apple see issue 33

You can download and install the current R package.

run R (>= 4.0) and type

# install required packages 
pkgs <- c('dplyr', 'hexbin', 'protViz', 'RSQLite', 'scales', 'tidyr', 'tidyverse', 'shiny')
pkgs <- pkgs[(!pkgs %in% unique(installed.packages()[,'Package']))]
if(length(pkgs) > 0){install.packages(pkgs)}

install rawDiag

install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawDiag_0.0.38.tar.gz', repo=NULL)

it should run out of the box. A possible first code snippet is below

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

After Install please send us an Email, SUBJECT rawDiag package.

What kind of instrument data do you use?

If you still have problems, please let us know via Email, SUBJECT request help rawDiag package.

Output of R's function sessionInfo()

New features

0. removed data used in our initial JPR publication

1. refactored read.raw.info

Proteomics Forum 2019

version 0.0.34

Thank you for your interest in the rawDiag package.

please use the build package.

If you accept the Thermo License agreement

https://github.com/fgcz/rawDiag/blob/master/inst/docker/ThermoRawFileReader/RawFileReaderLicense.doc

You can download and install the current R package.

run R (>= 3.5.1) and type

# install required packages 
pkgs <- c('dplyr', 'hexbin', 'protViz', 'RSQLite', 'scales', 'tidyr', 'tidyverse', 'shiny')
pkgs <- pkgs[(!pkgs %in% unique(installed.packages()[,'Package']))]
if(length(pkgs) > 0){install.packages(pkgs)}

install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawDiag_0.0.34.tar.gz', repo=NULL)

it should run out of the box. A possible first code snippet is below

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

After Install please send us an Email, SUBJECT rawDiag package.

What kind of instrument data do you use?

If you still have problems, please let us know via Email, SUBJECT request help rawDiag package.

Manuscript ID: pr-2018-001736.R1.

version 0.0.3

zip rawDiag.zip rawDiag.Rnw rawDiag.tex rawDiag.bib graphics/*

Manuscript ID: pr-2018-001736.

JPR

Update README.md