Run CCA in Seurat
I'm running CCA and I don't know why an error occurred in MergeSeurat. Any help is appreciated. Here's my code:
g.1 <- head(rownames(ctrl@hvg.info), 1000)
g.2 <- head(rownames(stim@hvg.info), 1000)
genes.use <- unique(c(g.1, g.2))
genes.use <- intersect(genes.use, rownames(ctrl@scale.data))
genes.use <- intersect(genes.use, rownames(stim@scale.data))
asthma.combined <- RunCCA(ctrl, stim, genes.use = genes.use, num.cc = 30)
Running CCA Merging objects Error in MergeSeurat(object1 = object, object2 = object2, do.scale = FALSE, : Duplicate cell names, please provide 'add.cell.id1' and/or 'add.cell.id2' for unique names
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The error message is quite clear:
Add the arguments add.cell.id1="ctrl",add.cell.id1="stim" to your RunCCA call. This will append these onto your ids.
You probably mean
add.cell.id1="ctrl",add.cell.id2="stim", no?