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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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Specify custom genes/features #78

Closed royfrancis closed 5 years ago

royfrancis commented 5 years ago

It's not very clear to me where is the sc3 workflow the feature selection happens. I have a list of highly variable genes that I would like to use for the sc3 clustering. Where/when do I specify this? Thanks.

wikiselev commented 5 years ago

Hi, yes, you can manually define genes that you want to use for clustering by setting the sc3_gene_filter column of the rowData slot. See some more description here. You can do:

rowData(sce)$sc3_gene_filter <- ... (a boolean vector with the selected genes corresponding to TRUE)