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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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How to use t-test and beta-binomial generalized linear model in package aod:: betabin to test the difference in cluster abundances (cell counts) between MS donors and control donors #3

Closed Jihong528 closed 3 years ago

Jihong528 commented 3 years ago

Hello, I am so sorry that I can't understand how to use the aod:: betabin package to test the difference in cluster abundances (cell counts) between MS donors and control donors. I have download the Betabinom.R from your github, but I can't find the count file(count = read.table(paste(filename, '.count.txt',sep=''))), so I don't know how to run the function, could you please provide the file? Thanks a lot for your help.

chenlingantelope commented 3 years ago

Hi Jihong, Sorry for the late reply. count.txt is a matrix that stores the number of cells per sample per cell type. The rows are each sample, and columns are cell types. I will upload it to the folder where the .R file is. Best, Chenling