From 97cb6f6f75426f4ae6af3287ef713a9b3312f101 Mon Sep 17 00:00:00 2001 From: Alan O'Callaghan Date: Tue, 4 Oct 2022 21:03:45 +0100 Subject: [PATCH] Revert "Revert "Cell-annotation fix for AUCell"" This reverts commit 3d68945eb98857995d0f8b506873b86fde0ed25e. --- inst/book/cell-annotation.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/book/cell-annotation.Rmd b/inst/book/cell-annotation.Rmd index c037569..c857379 100644 --- a/inst/book/cell-annotation.Rmd +++ b/inst/book/cell-annotation.Rmd @@ -221,7 +221,7 @@ all.sets <- GeneSetCollection(all.sets) library(AUCell) rankings <- AUCell_buildRankings(counts(sce.tasic), - plotStats=FALSE, verbose=FALSE) + plotStats=FALSE, verbose=FALSE, splitByBlocks = TRUE) cell.aucs <- AUCell_calcAUC(all.sets, rankings) results <- t(assay(cell.aucs)) head(results) @@ -284,7 +284,7 @@ For example, applying all of the MSigDB signatures on the Muraro dataset is rath muraro.mat <- counts(sce.muraro) rownames(muraro.mat) <- rowData(sce.muraro)$symbol muraro.rankings <- AUCell_buildRankings(muraro.mat, - plotStats=FALSE, verbose=FALSE) + plotStats=FALSE, verbose=FALSE, splitByBlocks = TRUE) # Applying MsigDB to the Muraro dataset, because it's human: scsig.aucs <- AUCell_calcAUC(scsigs, muraro.rankings)