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satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
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How to set n_genes in SCTransform #173

Closed SihanLiUVa closed 8 months ago

SihanLiUVa commented 8 months ago

Hi! According to the issue#124, I am trying to increase the number of genes in the function SCTransform. Here are my codes: group1 <- SCTransform(group1_data,vars.to.regress = "nCount_RNA", ncells = 5000, vst.flavor = "v2", return.only.var.genes = FALSE, n_genes = 5000) I noticed that in the argument of this function, the n_genes is supposed to pass to sctransform::vst, where the n_genes is used. However, i still got this message from my console. Get Negative Binomial regression parameters per gene Using 2000 genes Would you please teach me how to pass this argument? Thank you so much in advance!

saketkc commented 8 months ago

Duplicate of https://github.com/satijalab/seurat/issues/7998