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ACTIONet single-cell analysis framework
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assess.geneset.enrichment.from.archetypes returns 1 fewer genesets than given #5

Open dpcook opened 3 years ago

dpcook commented 3 years ago

I'm finding that the assess.geneset.enrichment.from.archetypes() function returns one fewer gene sets than provided in the membership matrix

ncol(membership_matrix)
> 10
tmp <- assess.geneset.enrichment.from.archetypes(action_list[[1]], associations = membership_matrix)
nrow(tmp$logPvals)
> 9

And it seems that it's always the geneset in the first column of the membership matrix that is lost

colnames(membership_matrix)[2:ncol(membership_matrix)] == rownames(tmp$logPvals)
> TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
shmohammadi86 commented 3 years ago

That's correct, there is a typo in it, which I'll push changes today. Thanks for reporting it

On Thu, Nov 12, 2020, 5:54 PM David Cook notifications@github.com wrote:

I'm finding that the assess.geneset.enrichment.from.archetypes() function returns one fewer gene sets than provided in the membership matrix

ncol(membership_matrix)

10

tmp <- assess.geneset.enrichment.from.archetypes(action_list[[1]], associations = membership_matrix) nrow(tmp$logPvals)

9

And it seems that it's always the geneset in the first column of the membership matrix that is lost

colnames(membership_matrix)[2:ncol(membership_matrix)] == rownames(tmp$logPvals)

TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

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