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https://github.com/cpanse/tartare

raw file collection recorded on Thermo Fisher Scientific mass spectrometers for extented unit testing

https://github.com/cpanse/tartare

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bioconductor blob data r unittesting
Last synced: 6 months ago · JSON representation

Repository

raw file collection recorded on Thermo Fisher Scientific mass spectrometers for extented unit testing

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bioconductor blob data r unittesting
Created over 6 years ago · Last pushed over 6 years ago
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Readme

README.md

tartare

raw file collection recorded on Thermo Fisher Scientific mass spectrometers for extented unit testing

https://github.com/Bioconductor/Contributions/issues/1286

install

```

Release (3.10)

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("tartare", version="devel") ```

see also https://bioconductor.org/packages/tartare/

requires

the following usage example requires the following packages:

  1. https://github.com/rformassspectrometry/Spectra
  2. https://github.com/cpanse/MsBackendRawFileReader

schema Courtesy of @jorainer; SWEMSA 2019 conference in Erding, Germany 10.5281/zenodo.3499649.

usage

taken from the help pages ?tartare.

``` library(tartare) library(ExperimentHub)

eh <- ExperimentHub() (files <- getFilename(eh))

library(MsBackendRawFileReader)

be <- lapply(files, function(f){ if (grepl("mzXML$", f)) backendInitialize(MsBackendMzR(), files = f) else backendInitialize(MsBackendRawFileReader(), files = f, extra=FALSE) })

be ```

``` R> be $EH3219 MsBackendMzR with 1764 spectra msLevel rtime scanIndex 1 1 0.215344 1 2 1 0.713714 2 3 1 1.10822 3 4 1 1.50284 4 5 1 1.89709 5 ... ... ... ... 1760 2 239.767 1760 1761 2 239.834 1761 1762 2 239.901 1762 1763 2 239.969 1763 1764 2 240.036 1764 ... 31 more variables/columns.

file(s): 203c4d41aa69_3235

$EH3220

filename: /Users/cp/Library/Caches/ExperimentHub/203c576b7cbf_3236.raw creation date: 7/11/2019 11:04:01 AM first scan: 1 last scan: 1877 model: Q Exactive HF-X Orbitrap name: Q Exactive HF-X Orbitrap SerialNumber: Exactive Series slot #6114

$EH3221 MsBackendMzR with 8742 spectra msLevel rtime scanIndex 1 1 0.0653085 1 2 1 0.392698 2 3 1 0.720055 3 4 1 1.04732 4 5 1 1.37468 5 ... ... ... ... 8738 1 2099.13 8738 8739 1 2099.44 8739 8740 1 2099.76 8740 8741 1 2100.07 8741 8742 1 2100.38 8742 ... 31 more variables/columns.

file(s): 203c51cb0c6f_3237

$EH3222

filename: /Users/cp/Library/Caches/ExperimentHub/24ab678291f6_3238.raw creation date: 7/16/2019 5:56:24 PM first scan: 1 last scan: 8742 model: Orbitrap Fusion Lumos name: Orbitrap Fusion Lumos SerialNumber: FSN20583

R> ```

hfx.filename <- getFilename(eh, c('tartar', '20190710_003_PierceHeLaProteinDigestStd.raw')); x <- .cnew ("Rawfile", hfx.filename); x$GetInfoValues()

see ?tartare and browseVignettes('tartare') for documentation downloading 0 resources loading from cache [1] "/Users/cp/Library/Caches/ExperimentHub/203c576b7cbf_3236.raw" [2] "7/11/2019 11:04:01 AM" [3] "1" [4] "1877" [5] "Q Exactive HF-X Orbitrap" [6] "Q Exactive HF-X Orbitrap" [7] "Exactive Series slot #6114"

Owner

  • Name: Christian Panse
  • Login: cpanse
  • Kind: user
  • Location: 47N 008E
  • Company: Swiss federal institute of technology in Zurich

proteome informatics; ms comp; visualization; maps; code; reproducible research @hb9feb@fosstodon.org

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Dependencies

DESCRIPTION cran
  • AnnotationHub >= 2.16 depends
  • ExperimentHub >= 1.0 depends
  • R >= 3.6 depends
  • utils * imports
  • BiocStyle * suggests
  • knitr * suggests
  • testthat * suggests
  • tools * suggests