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decomverse / ACTIONet

ACTIONet single-cell analysis framework
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Gene set scoring functions don't match vignette #2

Open dpcook opened 3 years ago

dpcook commented 3 years ago

Hi there--fantastic package! Really love its approach.

I'm just going through the vignette and have noticed that the gene set scoring functions may have changed since the vignette. I'm hoping to get geneset enrichment for each archetype along with cell-level scores for each.

Vignette for pathway activity scores:

Pathway.Enrichment = assess.geneset.enrichment(ace = ace, associations = nanoStringDB_human$Immunology)
cell.enrichment.scores = map.cell.scores.from.archetype.enrichment(ace, Pathway.Enrichment)

assess.geneset.enrichment() doesn't seem to exist anymore though. However, I think this has moved to assess.geneset.enrichment.from.archetypes(), which produces a list containing: $logPvals (is this -log10 or -log?), which has the pathway x archetype p-values, which is great $thresholds $scores a genes x archetypes matrix

Does map.cell.scores.from.archetype.enrichment() just want $logPvals, or is it looking for a pathway score x archetype matrix from some function??

shmohammadi86 commented 3 years ago

Hi David,

Thanks a lot for your feedback and for pointing this out. First of all, thresholds are the total number of top-ranked genes in that archetype, according to ace$unified_featured_specificity, that resulted in the most significant score. We are using a novel nonparametric enrichment method that was developed after ACTIONet original submission, thus is not in the main paper, but the implementation is here

Two points to mention: 1) scale is the natural log and all computations are performed in the log-space to avoid numerical under/over-flow, 2) These are technically upper-bounds on the p-value, which is computed using a closed-form analytical solution.

for the map.cell.scores.from.archetype.enrichment() function, it just needs the annotation x archetype enrichment from any type of enrichment analysis (pathway, markers, etc.)

Please let me know if you have any additional questions

On Tue, Oct 27, 2020 at 8:01 AM David Cook notifications@github.com wrote:

Hi there--fantastic package! Really love its approach.

I'm just going through the vignette and have noticed that the gene set scoring functions may have changed since the vignette. I'm hoping to get geneset enrichment for each archetype along with cell-level scores for each.

Vignette for pathway activity scores:

Pathway.Enrichment = assess.geneset.enrichment(ace = ace, associations = nanoStringDB_human$Immunology) cell.enrichment.scores = map.cell.scores.from.archetype.enrichment(ace, Pathway.Enrichment)

assess.geneset.enrichment() doesn't seem to exist anymore though. However, I think this has moved to assess.geneset.enrichment.from.archetypes(), which produces a list containing: $logPvals (is this -log10 or -log?), which has the pathway x archetype p-values, which is great $thresholds $scores a genes x archetypes matrix

Does map.cell.scores.from.archetype.enrichment() just want $logPvals, or is it looking for a pathway score x archetype matrix from some function??

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dpcook commented 3 years ago

This is great--thank you! One follow up: what function are you using to generate an annotation x archetype activity score matrix? I don't think I found one, but may have missed something.

Thanks!