Package: RaMS 1.4.3

RaMS: R Access to Mass-Spec Data

R-based access to mass-spectrometry (MS) data. While many packages exist to process MS data, many of these make it difficult to access the underlying mass-to-charge ratio (m/z), intensity, and retention time of the files themselves. This package is designed to format MS data in a tidy fashion and allows the user perform the plotting and analysis.

Authors:William Kumler [aut, cre, cph], Ricardo Cunha [ctb], Ethan Bass [ctb]

RaMS_1.4.3.tar.gz
RaMS_1.4.3.zip(r-4.7)RaMS_1.4.3.zip(r-4.6)RaMS_1.4.3.zip(r-4.5)
RaMS_1.4.3.tgz(r-4.6-any)RaMS_1.4.3.tgz(r-4.5-any)
RaMS_1.4.3.tar.gz(r-4.7-any)RaMS_1.4.3.tar.gz(r-4.6-any)
RaMS_1.4.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RaMS/json (API)

# Install 'RaMS' in R:
install.packages('RaMS', repos = c('https://wkumler.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wkumler/rams/issues

On CRAN:

Conda:

mass-spectrometry-datatidy-data

8.90 score 25 stars 8 packages 132 scripts 578 downloads 1 mentions 14 exports 5 dependencies

Last updated from:f6f3bb0b85. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK203
source / vignettesOK248
linux-release-x86_64OK201
macos-release-arm64OK217
macos-oldrel-arm64OK244
windows-develOK157
windows-releaseOK130
windows-oldrelOK159
wasm-releaseOK145

Exports:%between%betweeneditMSfileRTsgrabAccessionDatagrabMSdatagrabMzmlDatagrabMzxmlDataminifyMSdatamsdata_connectionmz_grouppmppmqplotMS1datatmzmlMakertrapz

Dependencies:base64encclidata.tablerlangxml2

Benchmarking - RaMS, MSnBase, Spectra, Arrow, and SQL
Intro | Original MSnExp | New onDiskMSnExp infrastructure | Spectra package | RaMS package | tmzML files | Arrow package | SQL(ite) | DuckDB | MS data transformation timings | MS data query timings | Multiple chromatograms | MS object sizing info | Summary
Rendered fromspeed_size_comparison.Rmdusingknitr::rmarkdown

Last update: 2024-10-09
Started: 2023-12-12

Introduction to the tmzML file type
What is tmzML? | Why tmzML? | Getting started with tmzML documents | Why not tmzML? | tmzML internals
Rendered fromIntro-to-tmzML.Rmdusingknitr::rmarkdown

Last update: 2024-10-09
Started: 2022-04-08

Minifying files with RaMS
Rendered fromMinifying-files-with-RaMS.Rmdusingknitr::rmarkdown

Last update: 2024-09-20
Started: 2022-04-08

Intro to RaMS
Basic RaMS usage | TICs, BPCs, and metadata | Adding a column: MS1 data | Moving along: MSn data | Continuing: chromatograms! | Advanced RaMS usage | Saving space: EICs and rtrange | Speeding things up | Finer control: grabMzmlData, grabMzxmlData | The nitty-gritty details
Rendered fromIntro-to-RaMS.Rmdusingknitr::rmarkdown

Last update: 2024-09-19
Started: 2021-03-16

RaMS and friends
Standard export to CSV | Fancier export to Excel | Exporting to SQL database | Interfacing with Python via reticulate | R code chunk: | Python code chunk:
Rendered fromRaMS-and-friends.Rmdusingknitr::rmarkdown

Last update: 2024-03-03
Started: 2021-01-31

Readme and manuals

Help Manual

Help pageTopics
S3 indexing for msdata_connection objects[.msdata_connection
S3 dollar sign notation for msdata_connection objects$.msdata_connection
Check that the output data is properly formatted.checkOutputQuality
Edit mzML/mzXML file retention timeseditMSfileRTs
Convert from compressed binary to R numeric vectorgetEncoded
Convert from R numeric vector to compressed binarygiveEncoding
Get arbitrary metadata from an mzML file by accession numbergrabAccessionData
Grab mass-spectrometry data from file(s)grabMSdata
Grab the BPC or TIC from a filegrabMzmlBPC
Extract the DAD data from an mzML nodesetgrabMzmlDAD
Get mass-spectrometry data from an mzML filegrabMzmlData
Helper function to extract mzML file encoding datagrabMzmlEncodingData
Helper function to extract mzML file metadatagrabMzmlMetadata
Extract the MS1 data from an mzML nodesetgrabMzmlMS1
Extract the MS2 data from an mzML nodesetgrabMzmlMS2
Extract the MS3 data from an mzML nodesetgrabMzmlMS3
Grab the BPC or TIC from a filegrabMzxmlBPC
Get mass-spectrometry data from an mzXML filegrabMzxmlData
Helper function to extract mzXML file metadatagrabMzxmlEncodingData
Helper function to extract mzXML file metadatagrabMzxmlMetadata
Extract the MS1 data from an mzXML nodesetgrabMzxmlMS1
Extract the MS2 data from an mzXML nodesetgrabMzxmlMS2
Extract the MS3 data from an mzXML nodesetgrabMzxmlMS3
Extract the mass-to-charge data from the spectra of an mzXML nodesetgrabMzxmlSpectraMzInt
Extract the precursor mass from the spectra of an mzXML nodesetgrabMzxmlSpectraPremz
Extract the retention time from the spectra of an mzXML nodesetgrabMzxmlSpectraRt
Extract the collision energies from the spectra of an mzXML nodesetgrabMzxmlSpectraVoltage
Extract the intensity information from the spectra of an mzML nodesetgrabSpectraInt
Extract the mass-to-charge data from the spectra of an mzML nodesetgrabSpectraMz
Extract the precursor mass from the spectra of an mzML nodesetgrabSpectraPremz
Extract the retention time from the spectra of an mzML nodesetgrabSpectraRt
Extract the collision energies from the spectra of an mzML nodesetgrabSpectraVoltage
Shrink MS data by including only data points near masses of interestminifyMSdata
Shrink mzML files by including only data points near masses of interestminifyMzml
Shrink mzXML files by including only data points near masses of interestminifyMzxml
S3 constructor for msdata_connectionmsdata_connection
Group m/z values into bins of a specified ppm widthmz_group
Convert node to data.tablenode2dt
Plus/minus parts per millionpmppm
S3 print option for msdata_connection objectsprint.msdata_connection
Quick plot for MS dataqplotMS1data
Maker of tmzML documentstmzmlMaker
Trapezoidal integration of mass-spec retention time / intensity valuestrapz