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chenlingantelope / MSscRNAseq2019

Analysis for 2019 submission "Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis" Schafflick1, Xu, Hartlehnert1 et. al
MIT License
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case/control and CSF/PBMC coding #8

Closed laleaton closed 1 month ago

laleaton commented 1 month ago

Hello, Thank you for providing your code and the .5ad file! I have converted this file into an h5 Seurat object in R using SeuratDisk and have successfully unpacked this integrated dataset. I have also been able to reproduce your figure 1b combined umap figure. I am now wanting to split the data into cases and tissues. I see in the object's metada an "MS" and "CSF" column with 1s and 2s. I am assuming these correspond to case or control and CSF vs PBMC. However, I am not able to find anywhere in your python code that notes how this is coded. Can you please advise? Thank you, Laura Ann Leaton

laleaton commented 1 month ago

solved by guessing which condition the 1/2 codes, subsetting the data, and checking plots against manuscript figures 1b and 2d

eg blood

object@meta.data(CSF == "1")

eg healthy

object@meta.data(MS == "1")