Loss of orthogroups after query_pangenes function?

jtlovell / GENESPACE

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Loss of orthogroups after query_pangenes function? #164

Closed FSU-pjtb closed 4 months ago

FSU-pjtb commented 4 months ago

In the REFERENCE_pangenes.txt output file, we have 27000 unique orthogroups ('og' column, syntenic and non-syntenic orthologs).

However after running query_pangenes(gsParam, refGenome = "REFERENCE"), we get an output with only 21000 unique orthogroups.

The query_pangenes table otherwise seems to be exactly what we need, so my question is what might be happening to the other 6000 orthogroups, and whether their loss is important.

Thank you!

FSU-pjtb commented 4 months ago

Nevermind - apparently the lost OGs are resulting from if (!showUnPlacedPgs) {out <- subset(out, !is.na(interpOrd))}, where showUnPlacedPgs defaults to FALSE.