Return all defined assay names

fmicompbio · Mar 5, 2023 · 7c05481 · 7c05481
1 parent dfec0e8
commit 7c05481
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Showing 4 changed files with 4 additions and 1 deletion.
diff --git a/inst/extdata/process_FragPipe_template.Rmd b/inst/extdata/process_FragPipe_template.Rmd
@@ -959,6 +959,7 @@ S4Vectors::metadata(sce) <- c(
     S4Vectors::metadata(sce), 
     list(
         fragpipeDir = fragpipeDir,
+        aNames = aNames, 
         aName = aNames$assayInput,
         iColPattern = iColPattern,
         imputeMethod = imputeMethod,

diff --git a/inst/extdata/process_MaxQuant_template.Rmd b/inst/extdata/process_MaxQuant_template.Rmd
@@ -948,6 +948,7 @@ S4Vectors::metadata(sce) <- c(
     S4Vectors::metadata(sce), 
     list(
         mqFile = mqFile,
+        aNames = aNames, 
         aName = aNames$assayInput,
         iColPattern = iColPattern,
         imputeMethod = imputeMethod,

diff --git a/inst/extdata/process_PD_TMT_template.Rmd b/inst/extdata/process_PD_TMT_template.Rmd
@@ -931,6 +931,7 @@ S4Vectors::metadata(sce) <- c(
     S4Vectors::metadata(sce), 
     list(
         pdFile = pdFile,
+        aNames = aNames, 
         aName = aNames$assayInput,
         iColPattern = iColPattern,
         imputeMethod = imputeMethod,

diff --git a/vignettes/einprot.Rmd b/vignettes/einprot.Rmd
@@ -442,7 +442,7 @@ not the columns corresponding to the test results that are copied into the
 row data of the returned object). The separate test results are included in the
 final `SingleCellExperiment` object and can be accessed via 
 ```{r, eval=FALSE}
-testres <- metadata(sce)$testres
+testres <- metadata(sce)$testres$tests
 ```
 (assuming that `sce` corresponds to the `SingleCellExperiment` object 
 returned by the `einprot` workflows).