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EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data

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Seurat_Pre_Process few issues

hanasusak opened this issue · comments

commented

at line #31 it returns data.frame with 0 columns:

expression[as.character(clusters2$X)]
data frame with 0 columns and 19081 rows

I think it is because you use capital X as a column and the clusters2 object has the column name 'x' inherited from clusters object:

head(clusters2)
cell x
1 AAACCTGCACATCCAA 2
3 AAACCTGCATCATCCC 2
4 AAACCTGGTAGCTCCG 2

Also, loading object clusters (at line #17) is tricky, as if you just save it from Seurat object, it will be loaded as 1 column data.frame, and I think you assume 2 columns. Additionally, it would be good to make sure that column cluster in genes data.frame, and column x in clusters data frame are numeric before adding 1.

commented

Facing the same problems

Also, I'm not sure why to add the +1 to the cluster ids which will be by default seurat@ident. It is true that by default they are just numbers from 0 up to number of clusters -1 but one can change them to be cell type names which are not numeric at all.