GSEA using DEG csv file obtained from seurat scRNA-seq data
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Entering edit mode
12 weeks ago
my.kim • 0

Hi,

I got DEG data from Seurat scRNA-seq and really want to draw the GSEA plot on Rstudio. I found the easiest method (https://bioinformaticsbreakdown.com/how-to-gsea/).

Here is the code I used.

tmp = read.csv("/Directory/DEG.csv", header = TRUE) %>% filter(Gene.Symbol !="")

Data.frame

> GO_file = "/Directory/c5.bp.v6.2.symbols.gmt" # I got this from http://www.gsea-msigdb.org/gsea/msigdb/collections.jsp

> gene_list = tmp$avg_log2FC

> names(gene_list) = tmp$Gene.Symbol

> gene_list = sort(gene_list, decreasing = TRUE)

> gene_list = gene_list[!duplicated(names(gene_list))]

> head(gene_list)

> res = GSEA(gene_list, GO_file, pval = 0.05) 

The very last step caused an error as follow.

> Error in build_Anno(TERM2GENE, TERM2NAME) :  argument "TERM2GENE" is missing, with no default

Do you guys figure out what's going on here? Could you add the code for me to complete this work?

Thank you.

GSEA scRNAseq dataframe seurat • 204 views
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