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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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Set filtering of genes to FALSE #100

Closed HaniJieunKim closed 3 years ago

HaniJieunKim commented 3 years ago

Hi!

Thanks for creating this package! I am running sctransform and realising it is doing some gene filtering in the backend.

Is it possible to set this to FALSE so that the same number of genes are retained?

Thanks in advance!

Best regards,

Hani

ChristophH commented 3 years ago

See #27 and #48

HaniJieunKim commented 3 years ago

Thanks. Is the min_cells parameter only found in sctransform::vst and not in Seurat::SCTransform? I can't seem to find the equivalent parameter in Seurat::SCTransform.

ChristophH commented 3 years ago

Note the ellipsis (...) in the Seurat::SCTransform function definition and its documentation:

... Additional parameters passed to sctransform::vst

Named arguments that do not match the arguments of Seurat::SCTransform will be passed to sctransform::vst, so you can use min_cells directly when calling Seurat::SCTransform

HaniJieunKim commented 3 years ago

Great thank you!