DEG analysis for multiple celltypes

[gitbuckley]

Hi, the documentation for your DEG function states "Differential expressed genes will be called within each cell type by the method users select." However, when I run it with data that has more than one cell type, I receive the error message "Error: please compare data with sinlge cell type" How do I generate figures like those found in Figure 2D of the associated bioRxiv paper? Sweet package by the way, thanks for developing.

[ywang65]

Hi,

You can write a loop to find DEGs each cell type separately, and then combine them together to find LRIs and do the plot. For finding LRIs, you can exclude autocrines by setting data_1 and data_2 in FindLR function, or you can include autocrines by setting data_2 NULL.

[fangling0913]

@ywang65 Hi, the DEG function compare the differential expressed genes between two samples in one cell type. However, I want to compare differential expressed genes between two cell type in one sample and use these genes to get cell interaction network. How can I do it in iTALK?

[ywang65]

Then you may want to change the colnames of matrix/dataframe a little bit to make the samples cell type and cell type samples.