Package 'tartare'

Title: Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers
Description: Provides raw files recorded on different Liquid Chromatography Mass Spectrometry (LC-MS) instruments. All included MS instruments are manufactured by Thermo Fisher Scientific and belong to the Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their common origin and shared hardware components, e.g., Orbitrap mass analyser, the above instruments tend to write data in different "dialects" in a shared binary file format (.raw). The intention behind tartare is to provide complex but slim real-world files that can be used to make code robust with respect to this diversity. In other words, it is intended for enhanced unit testing. The package is considered to be used with the rawrr package and the Spectra MsBackends.
Authors: Christian Panse [aut, cre] (ORCID: <https://orcid.org/0000-0003-1975-3064>), Tobias Kockmann [aut] (ORCID: <https://orcid.org/0000-0002-1847-885X>)
Maintainer: Christian Panse <[email protected]>
License: GPL-3
Version: 1.26.0
Built: 2026-10-10 11:13:18 UTC
Source: https://github.com/bioc/tartare

Help Index

downloads files from aws storage and returns local filepath

Description

calls the query method of an ExperimentHub object query and returns the local filenames. Of note: for proprietary reasons, a file.link is set to the cached files. It seems that the New RawfileReader .Net library is only accepting files ending with raw. The overall file size is 285MB.

Usage

getFilename(eh, query = c("tartare"))

Arguments

eh

ExperimentHub object.
query

a query string, e.g., c('tartar', '20190710_003_PierceHeLaProteinDigestStd.raw')

Value

returns file(s) contained in the tartare package.

Author(s)

Christian Panse <[email protected]>, 2019-10

See Also

  • browseVignettes('tartare')

  • query

Examples

library(ExperimentHub)
eh <- ExperimentHub()
query(eh, c('tartare'))

## Not run: 
(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)
})

## End(Not run)

## Not run: 
hfx.filename <- .query(eh, c('tartar', '20190710_003_PierceHeLaProteinDigestStd.raw'))
x <- .cnew ("Rawfile", hfx.filename)
x$GetInfoValues()

## End(Not run)