diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 99665ed..8137f93 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -53,8 +53,8 @@ jobs: matrix: config: - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } - - { os: macOS-latest, r: '4.4', bioc: '3.19'} - - { os: windows-latest, r: '4.4', bioc: '3.19'} + - { os: macOS-latest, r: '4.4', bioc: 'devel'} + - { os: windows-latest, r: '4.4', bioc: 'devel'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} diff --git a/DESCRIPTION b/DESCRIPTION index 53f0a42..16726cb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: SpectraQL Title: MassQL support for Spectra -Version: 0.98.6 +Version: 0.99.0 Description: The Mass Spec Query Language (MassQL) is a domain-specific language enabling to express a query and retrieve mass spectrometry (MS) data in a more natural and understandable way for MS users. It is inspired @@ -21,7 +21,7 @@ Authors@R: c(person(given = "Johannes", family = "Rainer", comment = c(ORCID = "0000-0001-7406-4443")) ) Depends: - R (>= 4.1.0), + R (>= 4.4.0), ProtGenerics (>= 1.25.1) Imports: Spectra (>= 1.5.6), diff --git a/R/AllGenerics.R b/R/AllGenerics.R index cd77443..77fb0d9 100644 --- a/R/AllGenerics.R +++ b/R/AllGenerics.R @@ -1,2 +1,2 @@ setGeneric("query", function(x, ...) - standardGeneric("query")) + standardGeneric("query")) diff --git a/vignettes/SpectraQL.Rmd b/vignettes/SpectraQL.Rmd index bf9dbce..1558787 100644 --- a/vignettes/SpectraQL.Rmd +++ b/vignettes/SpectraQL.Rmd @@ -37,9 +37,6 @@ for MS data represented by `Spectra` objects defined in Bioconductor's # Installation -Until added to Bioconductor, the package can be installed with -`devtools::install_github("RforMassSpectrometry/SpectraQL")`. - The package can be installed with the `BiocManager` package. To install `BiocManager` use `install.packages("BiocManager")` and, after that, `BiocManager::install("SpectraQL")` to install this package. @@ -309,9 +306,10 @@ We can also combine that with `"QUERY"` to restrict to a certain retention time range to generate an extracted ion chromatogram (XIC). ```{r} -ic <- query(dda, - paste0("query scansum(ms1data) where rtmin = 235 and rtmax = 250", - " filter ms1mz = 219.095:tolerancemz=0.1")) +ic <- query( + dda, + paste0("query scansum(ms1data) where rtmin = 235 and rtmax = 250", + " filter ms1mz = 219.095:tolerancemz=0.1")) plot(ic, type = "l", xlab = "scan index") ``` @@ -320,10 +318,10 @@ following combination of function calls: ```{r} res <- dda |> -filterMsLevel(1L) |> -filterRt(c(235, 250)) |> -filterMzValues(219.095, tolerance = 0.1) |> -ionCount() + filterMsLevel(1L) |> + filterRt(c(235, 250)) |> + filterMzValues(219.095, tolerance = 0.1) |> + ionCount() plot(res, type = "l", xlab = "scan index") ```