https://github.com/cpanse/tartare
raw file collection recorded on Thermo Fisher Scientific mass spectrometers for extented unit testing
https://github.com/cpanse/tartare
bioconductor blob data r unittesting
Last synced: 3 months ago
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raw file collection recorded on Thermo Fisher Scientific mass spectrometers for extented unit testing
- Host: GitHub
- URL: https://github.com/cpanse/tartare
- Owner: cpanse
- Created: 2019-07-22T13:48:51.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2019-10-28T14:31:19.000Z (over 5 years ago)
- Last Synced: 2025-02-08T16:28:45.422Z (5 months ago)
- Topics: bioconductor, blob, data, r, unittesting
- Language: R
- Homepage: https://bioconductor.org/packages/devel/data/experiment/html/tartare.html
- Size: 63.5 KB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 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
Courtesy of [@jorainer](https://github.com/jorainer); SWEMSA 2019 conference in Erding, Germany [10.5281/zenodo.3499649](https://doi.org/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"
```