fgsea_plot: Function to run fGSEA using the mSIGDB database from Broad

In brucemoran/RNAseqR: RNAseq DE Analysis Downstream from Nextflow Pipelines

Description

Function to run fGSEA using the mSIGDB database from Broad

fgsea plotting

Usage

fgsea_plot(fgsea_res_tb, msigdb_cat)

fgsea_plot(fgsea_res_tb, msigdb_cat)

Arguments

fgsea_res_tb	tibble of results from fgsea::fgsea
msigdb_cat	one of 'c("H", paste0("C", c(1:7)))', see: gsea-msigdb.org/gsea/msigdb/collections.jsp
res	output table from 'DESeq2_module()' (all genes not just sig)
sig_res	output table from 'DESeq2/limma/edger_module()' or combination thereof (used for table output)
msigdb_species	one of msigdbr::msigdbr_show_species(), default:"Homo sapiens"
gene_col	the name of the column in tibble with gene names found in pathways, set to "rownames" if they are the rownames (default)
rank_col	the name of the column in tibble which ranks genes for fgsea (default: "stat" for DESeq2 results; limma - use "t", edgeR - unsure)
padj	the significance threshold
output_dir	path to where output goes
tag	string used to prefix output
contrast	string to define the contrast being made, tags output

Value

msigdb_fgsea object

msigdb_pathlist list object

brucemoran/RNAseqR documentation built on Sept. 14, 2021, 11:08 a.m.