FindAllMarkers for all genes in Seurat
I want to use the FindAllMarkers function because I want pct1 and avg_logFC for each gene in my object. Here are the current parameters I am running:
data.markers <- FindAllMarkers(x=data, only.pos = FALSE, min.pct = 0, logfc.threshold = 0)
However, it only returns a subset of genes (about 3000). Why is this?
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Thorerges •
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Try adding
return.thresh = 1.01, as it looks like the default value is 0.01