From 84bb9011aaafb637ccc1fb462a66d498a09e7ea5 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 4 Mar 2024 09:26:56 -0800 Subject: [PATCH] Autodownload TCR data if missing --- singlecell/resources/chunks/SummarizeTCellActivation.R | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/singlecell/resources/chunks/SummarizeTCellActivation.R b/singlecell/resources/chunks/SummarizeTCellActivation.R index 0a373476d..ae7fa52d8 100644 --- a/singlecell/resources/chunks/SummarizeTCellActivation.R +++ b/singlecell/resources/chunks/SummarizeTCellActivation.R @@ -10,6 +10,10 @@ for (datasetId in names(seuratObjects)) { printName(datasetId) seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) + if (!'HasCDR3Data' %in% names(seuratObj@meta.data)){ + seuratObj <- seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = FALSE) + } + outFile <- paste0(outputPrefix, '.', makeLegalFileName(datasetId), '.activation.txt') Rdiscvr::SummarizeTNK_Activation(seuratObj, outFile = outFile, xFacetField = xFacetField, groupingFields = groupingFields, activationFieldName = activationFieldName, threshold = threshold)