FindMarkers for ClusterProfiler
1
0
Entering edit mode
3.1 years ago
cgp09741 ▴ 10

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.

ClusterProfiler gseGO enrichGO • 3.4k views
ADD COMMENT
0
Entering edit mode
3.1 years ago
Pratik ★ 1.0k

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

ADD COMMENT
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1806 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6