FindMarkers for ClusterProfiler

Question

[cgp09741]

Hi,

I recently ran FindMarkers to compare DEG between two different clusters in a single-cell RNA-seq analysis

This is my code:

markers= FindMarkers(obj, ident.1=c(4), ident.2 = c(5))
head(markers)
dim(markers)
table(markers$avg_log2FC > 0)
table(markers4v5$p_val_adj < 0.05 & markers$avg_log2FC > 0)

I would like to run ClusterProfiler to determine differentially expressed pathways between the two different clusters. I did not run DEseq2 like the tutorial online, so just have the parameters provided from FindMarkers... p_val, avg_log2FC, p_val_adj.

Is it okay to use the p_val, avg_log2FC and gene symbol in a csv file to develop my df function and gene_list/genes and then run gseGO and enrichGO commands?

Thank you.

Answer 1

[Pratik]

Hey, check this out:

How to transform the deg gene list from seurat to a gene list input to clusterProfiler compareCluster ?

I did something similar there, except for all clusters.

Basically the thought process is, on your filtered dataframe that has your markers (genes) filtered by your log2FC cut-off and your pval_adj cut-off. You want to convert those gene names over to ENTREZID (HGNC to ENTREZID), and then, make a list of your resulting ENTREZID and clusters and plug that list into ClusterProfiler.

You should check out that tutorial I wrote using the the standard Seurat pbmc dataset. Maybe run it through one time and do some exploration to understand it, and you should have success.

Good luck!

-Pratik

[cgp09741]

Great, thank you so much for your help. I will run through it and reach back out if I have any other questions!