diff --git a/inst/extdata/process_FragPipe_template.Rmd b/inst/extdata/process_FragPipe_template.Rmd index d661de9..91fc8b4 100755 --- 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$assayInput, iColPattern = iColPattern, imputeMethod = imputeMethod, diff --git a/inst/extdata/process_MaxQuant_template.Rmd b/inst/extdata/process_MaxQuant_template.Rmd index 9e7d098..e70b248 100755 --- a/inst/extdata/process_MaxQuant_template.Rmd +++ b/inst/extdata/process_MaxQuant_template.Rmd @@ -948,6 +948,7 @@ S4Vectors::metadata(sce) <- c( S4Vectors::metadata(sce), list( mqFile = mqFile, + aNames = aNames, aName = aNames$assayInput, iColPattern = iColPattern, imputeMethod = imputeMethod, diff --git a/inst/extdata/process_PD_TMT_template.Rmd b/inst/extdata/process_PD_TMT_template.Rmd index 49c426c..4526914 100644 --- 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$assayInput, iColPattern = iColPattern, imputeMethod = imputeMethod, diff --git a/vignettes/einprot.Rmd b/vignettes/einprot.Rmd index 67e9e36..0e719f3 100644 --- a/vignettes/einprot.Rmd +++ b/vignettes/einprot.Rmd @@ -442,7 +442,7 @@ not the columns corresponding to the test results that are copied into the row data of the returned object). The separate test results are included in the final `SingleCellExperiment` object and can be accessed via ```{r, eval=FALSE} -testres <- metadata(sce)$testres +testres <- metadata(sce)$testres$tests ``` (assuming that `sce` corresponds to the `SingleCellExperiment` object returned by the `einprot` workflows).