diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 0f1d68c..5b5bbf1 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -231,10 +231,10 @@ jobs: # cd preprocessCore # R CMD INSTALL --configure-args="--disable-threading" . - # - name: Manually install latest QFeatures - # run: | - # BiocManager::install("RforMassSpectrometry/QFeatures") - # shell: Rscript {0} + - name: Manually install latest RforMassSpectrometry/QFeatures + run: | + BiocManager::install("RforMassSpectrometry/QFeatures") + shell: Rscript {0} - name: Session info run: | diff --git a/DESCRIPTION b/DESCRIPTION index 65a343a..9e2394f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,7 +20,7 @@ Description: Utility functions for manipulating, processing, and visualization. Depends: R (>= 4.3.0), - QFeatures (>= 1.3.5) + QFeatures (>= 1.13.5) Imports: dplyr, IHW, diff --git a/vignettes/scp.Rmd b/vignettes/scp.Rmd index 8dd8507..ef43d45 100644 --- a/vignettes/scp.Rmd +++ b/vignettes/scp.Rmd @@ -171,7 +171,7 @@ table(sampleAnnotation$SampleType) Using `readSCP`, we combine both tables in a `QFeatures` object formatted as described above. -```{r readSCP2} +```{r readSCP} scp <- readSCP(assayData = mqScpData, colData = sampleAnnotation, runCol = "Raw.file", @@ -183,7 +183,7 @@ See here that the 3 first assays contain 11 columns that correspond to the TMT-11 labels and the last assay contains 16 columns that correspond to the TMT-16 labels. -**Important**: More details about the usage of `readSCP` and how to +**Important**: More details about the usage of `readSCP()` and how to read your own data set are provided in the `Load data using readSCP` [vignette](https://uclouvain-cbio.github.io/scp/articles/read_scp.html).