update vignette

rformassspectrometry · Apr 9, 2024 · b747013 · b747013
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MsDataHub
 Title: Mass Spectrometry Data on ExperimentHub
-Version: 1.3.3
+Version: 1.3.4
 Authors@R:
     c(person(given = "Laurent",
              family = "Gatto",
@@ -36,7 +36,7 @@ Suggests:
     Spectra,
     mzR,
     PSMatch,
-    QFeatures
+    QFeatures (>= 1.13.3)
 biocViews: ExperimentHubSoftware,
            MassSpectrometry,
            Proteomics,

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 # MsDataHub 1.3
 
+## MsDataHub 1.3.4
+
+- Update vignette: load `Report.Derks2022.plexDIA.tsv` and
+  `benchmarkingDIA.tsv` with latest QFeatures.
+
 ## MsDataHub 1.3.3
 
 - Add `Report.Derks2022.plexDIA.tsv`, plexDIA DIA-NN output from Derks

diff --git a/R/derks2022plexDIA.R b/R/derks2022plexDIA.R
@@ -1,6 +1,8 @@
 ##' @title Derks 2022 plexDIA data
 ##'
-##' @name Report.Derks2022.plexDIA.tsv
+##' @name Report.Derks2022.plexDIA
+##'
+##' @aliases Report.Derks2022.plexDIA.tsv
 ##'
 ##' @description
 ##'

diff --git a/man/Report.Derks2022.plexDIA.Rd b/man/Report.Derks2022.plexDIA.Rd
diff --git a/man/benchmarkingDIA.Rd b/man/benchmarkingDIA.Rd
diff --git a/vignettes/MsDataHub.Rmd b/vignettes/MsDataHub.Rmd
@@ -148,8 +148,28 @@ Spectra(f)
 
 ## DIA-NN software outputs
 
-- Label-free DIA: `benchmarkingDIA.tsv`
-- mTRAQ plexDIA: `Report.Derks2022.plexDIA.tsv`
+- Type: tab-delimited DIA quantitative proteomics data tables produced
+  by [DIA-NN](https://github.com/vdemichev/DiaNN).
+- Files:
+  - Label-free DIA: `benchmarkingDIA.tsv`
+  - mTRAQ plexDIA: `Report.Derks2022.plexDIA.tsv`
+- More details: `?benchmarkingDIA.tsv` and
+  `?Report.Derks2022.plexDIA.tsv`
+
+Load with
+
+```{r lfdia, eval = TRUE, message = FALSE}
+library(QFeatures)
+lfdia <- read.delim(MsDataHub::benchmarkingDIA.tsv())
+readQFeaturesFromDIANN(lfdia)
+```
+
+```{r pledia, eval = TRUE, message = FALSE}
+plexdia <- read.delim(MsDataHub::Report.Derks2022.plexDIA.tsv())
+readQFeaturesFromDIANN(plexdia, multiplexing = "mTRAQ")
+```
+
+
 
 # Adding data to `MsDataHub`