FindMarkers for ClusterProfiler
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?
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