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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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Doubt Integratedata using normalization SCTransform #138

Closed PilanEli closed 2 years ago

PilanEli commented 2 years ago

Hi,

I'm running the vignette and when I apply the functions for two condictions ( control and tumor) in the same dataset:

immune.anchors <- FindIntegrationAnchors(object.list = ifnb.list, normalization.method = "SCT", anchor.features = features) immune.combined.sct <- IntegrateData(anchorset = immune.anchors, normalization.method = "SCT")

The function integrateData this case with normalization SCtransform be changed to integrate data and keep full geneset (features.to.integrate = to_integrate)?

Thanks

PilanEli commented 2 years ago

I got it as follows: immune.combined.sct <- IntegrateData(anchorset = immune.anchors, (integrated_all_genes = T), normalization.method = "SCT")

I hope I'm right.

saketkc commented 2 years ago

I am not sure if I am understanding your question correctly, but by default IntegrateData will only integrate the features used in anchor finding. You can provide a custom list of features using features.to.integrate, see the documentation here. For future Integration questions, please open an issue in the Seurat repository.

PilanEli commented 2 years ago

Hi

Thank you so much. That was the doubt. I wrote here because I was in doubt for being inside the SCTransform script.

Best regards,