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It might be worth noting that sc3_prepare() adds the sc3_gene_filter column to rowData(object) if gene_filter = TRUE (in addition to creating and populating the metadata(object)).
I had trouble tracking down an error (a user error on my part) because I ran sc3_estimate_k() before and after running sc_prepare() and obtained different values due to the gene_filter; I couldn't figure out how to reconcile the two result based on the docs but realised the source (and my error) once I compared the before/after objects using all.equal().
Cheers,
Pete
The text was updated successfully, but these errors were encountered:
PeteHaitch
changed the title
Documentation of sc3_prepare()
Small suggestion for sc3_prepare() documentation
Sep 25, 2018
Hi,
Thanks for your work developing SC3!
It might be worth noting that
sc3_prepare()
adds thesc3_gene_filter
column torowData(object)
ifgene_filter = TRUE
(in addition to creating and populating themetadata(object)
).I had trouble tracking down an error (a user error on my part) because I ran
sc3_estimate_k()
before and after runningsc_prepare()
and obtained different values due to thegene_filter
; I couldn't figure out how to reconcile the two result based on the docs but realised the source (and my error) once I compared the before/after objects usingall.equal()
.Cheers,
Pete
The text was updated successfully, but these errors were encountered: