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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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Small suggestion for sc3_prepare() documentation #80

Open PeteHaitch opened 5 years ago

PeteHaitch commented 5 years ago

Hi,

Thanks for your work developing SC3!

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

wikiselev commented 5 years ago

Hi Pete, thanks for your feedback! Could you please create a pull request? (sorry, I literally have no time to work on SC3 anymore...)