search

saeyslab / multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
GNU General Public License v3.0
112 stars 14 forks source link

Setting multiple covariates and batches in multinichnet #26

Closed iichelhadi closed 1 year ago

iichelhadi commented 1 year ago

as per title. Was wondering how to set multiple covariates and batches for batch correction?

Thank you

browaeysrobin commented 1 year ago

Hi @iichelhadi

Multiple covariates: just make a vector of length > 1; should be fine. Let me know if not (then: give detail about the nature of the covariates etc) Multiple batches: not possible, you can make a new column in the metadata combining your different batches.

iichelhadi commented 1 year ago

thank you for the quick reply. I have integrated scRNA-seq datasets using harmony in a Seurat obj. I was thinking I should add "nCount_RNA", "nFeature_RNA" and "percent.mt" as covariates. I am not sure about the syntax I should be using.

something like this? c("nCount_RNA", "nFeature_RNA" , "percent.mt")