Package: RaMS 1.4.3

William Kumler

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.tar.gz(r-4.5-noble)RaMS_1.4.3.tar.gz(r-4.4-noble)
RaMS_1.4.3.tgz(r-4.4-emscripten)RaMS_1.4.3.tgz(r-4.3-emscripten)
RaMS.pdf |RaMS.html✨
RaMS/json (API)
NEWS

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

Peer review:

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

5.05 score 5 packages 84 scripts 460 downloads 1 mentions 14 exports 5 dependencies

Last updated 2 months agofrom:a84e188fa9. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 09 2024
R-4.5-linuxOKDec 09 2024

Exports:%between%betweeneditMSfileRTsgrabAccessionDatagrabMSdatagrabMzmlDatagrabMzxmlDataminifyMSdatamsdata_connectionmz_grouppmppmqplotMS1datatmzmlMakertrapz

Dependencies:base64encclidata.tablerlangxml2

Benchmarking - RaMS, MSnBase, Spectra, Arrow, and SQL

William Kumler

Rendered fromspeed_size_comparison.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2024-10-09
Started: 2023-12-14

Intro to RaMS

Rendered fromIntro-to-RaMS.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2024-10-09
Started: 2021-03-22

Introduction to the tmzML file type

Rendered fromIntro-to-tmzML.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2024-10-09
Started: 2022-11-28

Minifying files with RaMS

Rendered fromMinifying-files-with-RaMS.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2024-10-09
Started: 2022-11-28

RaMS and friends

Rendered fromRaMS-and-friends.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2024-03-03
Started: 2021-03-22

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