Mass Spec Query Language Support to the Spectra Package (original) (raw)

Package: SpectraQL
Authors: Johannes Rainer [aut, cre] (ORCID:https://orcid.org/0000-0002-6977-7147), Andrea Vicini [aut], Sebastian Gibb [ctb] (ORCID: https://orcid.org/0000-0001-7406-4443)
Compiled: Wed May 21 19:25:08 2025

Introduction

The Mass Spec Query Language (MassQL) is a domain specific language meant to be a succinct way to express a query in a mass spectrometry (MS) centric fashion. It is inspired by SQL, but it attempts to bake in assumptions of MS to make querying much more natural for MS users.

The SpectraQL package provides support for the MassQL language in R, for MS data represented by Spectra objects defined in Bioconductor’sSpectra package.

Installation

The package can be installed with the BiocManager package using:

## Install BiocManager, if not already installed
install.packages("BiocManager")
## Install the package
BiocManager::install("SpectraQL")

Session information

## R version 4.5.0 RC (2025-04-04 r88126)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] msdata_0.48.0       SpectraQL_1.2.1     ProtGenerics_1.40.0
## [4] Spectra_1.18.1      BiocParallel_1.42.0 S4Vectors_0.46.0   
## [7] BiocGenerics_0.54.0 generics_0.1.4      BiocStyle_2.36.0   
## 
## loaded via a namespace (and not attached):
##  [1] jsonlite_2.0.0         compiler_4.5.0         BiocManager_1.30.25   
##  [4] tinytex_0.57           Rcpp_1.0.14            Biobase_2.68.0        
##  [7] magick_2.8.6           parallel_4.5.0         cluster_2.1.8.1       
## [10] jquerylib_0.1.4        IRanges_2.42.0         yaml_2.3.10           
## [13] fastmap_1.2.0          R6_2.6.1               knitr_1.50            
## [16] MASS_7.3-65            bookdown_0.43          bslib_0.9.0           
## [19] rlang_1.1.6            cachem_1.1.0           xfun_0.52             
## [22] fs_1.6.6               MsCoreUtils_1.20.0     sass_0.4.10           
## [25] cli_3.6.5              magrittr_2.0.3         ncdf4_1.24            
## [28] digest_0.6.37          mzR_2.42.0             MetaboCoreUtils_1.16.1
## [31] lifecycle_1.0.4        clue_0.3-66            evaluate_1.0.3        
## [34] codetools_0.2-20       rmarkdown_2.29         tools_4.5.0           
## [37] htmltools_0.5.8.1