other_documents/prepare_example_GMT_file.md

In romanhaa/cerebroApp: Interactive visualization of scRNA-seq data with Cerebro

How to generate the example GMT file

The GMT file contains 20 genes present in the example Seurat PBMC data set to ensure the performGeneSetEnrichmentAnalysis() function will work properly. Storing gene sets in the GMT format requires a name, a description (here we used a URL), followed by the genes which belong to the set. All elements are separated by tabs. One gene set per line.

I have taken random genes from the Cerebro v1.3 example data set as shown below.

pbmc <- read.table(file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat'), as.is = TRUE)
sample(rownames(pbmc), 20)

romanhaa/cerebroApp documentation built on Nov. 25, 2021, 5:29 p.m.