N/A in DEGs and converting Seurat DEG to dataframe for FindLR

[Jennifer-Foltz]

Good morning! I am really enjoying trying out your new package! I have 2 questions about some of the output I've been receiving:

1). What are the NAs in the DEG output? How should this be interpreted?

2. I would like to be able to use the DEG results from Seurat in iTALK, so I converted the output FindMarkers in Seurat to a dataframe matching the input columns needed for FindLR, however, I am receiving the following warning message: Can you help me understand what this means?

Thank you very much for your time and help and for making this package!

[ywang65]

Hi! Thanks for your interest!

For your first question, what method did you use for finding the DEGs? You may able to find some insights from the original documents of the method.

And for the second question, these warnings just tell you one of the data type you try to join is factor and the other is character. After this join operation, the data type of the output will be changed into character. You can change them into factor again by using as.factor(df$column) if necessary

[Jennifer-Foltz]

Hi @ywang65 ! Thank you so much for your quick reply!

I used the Wilcox method for the DEGS: deg_nk<-DEG(data2 %>% filter(cell_type=='cd56_nk'),method='Wilcox',contrast=c(2,1))(trying out the vignette code), I also see them in the FindLR output if the gene had a NA in the DEG output. Can you point me to the original documents for the DEGs?

For the second question, thank you for the clarification! The results I get after this warning are an empty table, if I'm understanding correctly, this means that no ligand-receptor pairs were found and is not a product of the warning?

Thank you!