Package: opentimsr 1.2.0

Mateusz Krzysztof Łącki

opentimsr: An Open-Source Loader for Bruker's timsTOF Data Files

Reads raw data from Bruker's timsTOF mass spectrometers, stored in analysis.tdf and analysis.tdf_bin files inside .d folders. Frames can be selected by number or by retention time, and each peak is reported with its scan, time-of-flight index, intensity, mass-to-charge ratio and inverse ion mobility. Mass-to-charge ratios and ion mobilities are computed with built-in open-source calibration, or optionally with Bruker's proprietary library. See Łącki et al. (2021) <doi:10.1021/acs.jproteome.0c00962>.

Authors:Michał Piotr Startek [aut, cph], Mateusz Krzysztof Łącki [aut, cre, cph], mandreyel [ctb, cph]

opentimsr_1.2.0.tar.gz
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opentimsr_1.2.0.tar.gz(r-4.7-arm64)opentimsr_1.2.0.tar.gz(r-4.7-x86_64)opentimsr_1.2.0.tar.gz(r-4.6-arm64)opentimsr_1.2.0.tar.gz(r-4.6-x86_64)
opentimsr_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
opentimsr/json (API)

# Install 'opentimsr' in R:

install.packages('opentimsr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/michalsta/opentims/issues

Uses libs:

libzstd– Fast lossless compression algorithm
c++– GNU Standard C++ Library v3

On CRAN:

libzstd cpp

1.62 score 1 packages 14 scripts 19 exports 16 dependencies

Last updated from:82141cd2b7. Checks:10 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	147
linux-devel-x86_64	OK	120
source / vignettes	OK	215
linux-release-arm64	OK	108
linux-release-x86_64	OK	279
windows-devel-arm64	OK	194
windows-devel-x86_64	OK	173
windows-release-arm64	OK	228
windows-release-x86_64	OK	120
wasm-release	OK	140

Exports:CloseTIMS download_bruker_proprietary_code explore.tdf.tables get_separate_frames min_max_measurements MS1 OpenTIMS opentims_set_threads peaks_per_frame_cnts query query_slice retention_times rt_query setup_bruker_so setup_opensource table2df tables_names use_inv_ion_mobility_lookup use_mz_lookup

Dependencies:bit bit64 blob cachem cli cpp11 DBI fastmap glue lifecycle memoise pkgconfig Rcpp rlang RSQLite vctrs

Help page	Topics
Get some frames of data.	[,OpenTIMS-method
Close the TIMS data handle and release all resources.	CloseTIMS
Get Bruker's code needed for running proprietary time of flight to mass over charge and scan to drift time conversion.	download_bruker_proprietary_code
Explore the contentents of the sqlite .tdf database.	explore.tdf.tables
Get frames as separate data frames.	get_separate_frames
Get the overall number of peaks.	length,OpenTIMS-method
Get border values for measurements.	min_max_measurements
Get MS1 frame numbers.	MS1
Get OpenTIMS data representation.	OpenTIMS
Set the number of threads to be used for data processing by OpenTIMS	opentims_set_threads
TimsTOF data accessor.	OpenTIMS-class
Get the number of peaks per frame.	peaks_per_frame_cnts
Query for raw data.	query
Query for raw data.	query_slice
Select a range of frames to extract.	range,OpenTIMS-method
Get the retention time for each frame.	retention_times
Get the retention time for each frame.	rt_query
Dynamically link Bruker's DLL to enable tof-mz and scan-inv_ion_mobility conversion.	setup_bruker_so
Use the built-in open-source tof-to-mz and scan-to-inv_ion_mobility converters.	setup_opensource
Extract tables from sqlite database analysis.tdf.	table2df
Extract tables from sqlite database analysis.tdf.	tables_names
Use a lookup table for inverse ion mobility conversion with Bruker's library.	use_inv_ion_mobility_lookup
Use a lookup table for m/z conversion with Bruker's library.	use_mz_lookup

Package: opentimsr 1.2.0

opentimsr: An Open-Source Loader for Bruker's timsTOF Data Files

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)