In broadinstitute/cdsr_gsea: CDS function for gene set enrichment analysis

knitr::opts_chunk$set(warning = FALSE, message = FALSE, fig.width = 7, fig.height = 5, cache = T)

library(tidyverse)
library(useful)
library(taigr)
library(cdsrgsea)
library(cdsrplots)

cdsrgsea contains lightweight wrappers around useful gene set enrichment functions

Install

library(devtools)
devtools::install_github("broadinstitute/cdsr_gsea")

The package can then be loaded by calling

library(cdsrgsea)

gene_sets <- cdsrgsea::load_gene_sets()

load_gene_sets

Loads a list of gene sets in term2gene format from taiga. These gene sets are drawn from the Enrichr and MSigDB libraries.

gene_sets <- cdsrgsea::load_gene_sets()

gene_sets %>% names() %>% head()

gene_sets$Hallmark %>% head()

run_hyper

run_hyper runs overrepresentation analysis based on the hypergeometric distribution. The function excepts either a small list of significant genes or a table with gene level stats as input. If a table is provided the gene_var, rank_var, and n_genes parameters are used to define a small list of significant genes.

As an example we will load the results of a differential expression anlyses comparing Nutlin treated cells to DMSO treated cells.

nutlin <- read_csv("./nutlin.csv")
nutlin %>% head()

1. Small list of significant genes

genes <- nutlin %>% arrange(-logFC) %>% head(100) %>% .[["Gene"]]
genes %>% head()

hyper_res <- cdsrgsea::run_hyper(genes,gene_sets$Hallmark,universe = nutlin$Gene)
hyper_res

1. A table with gene level stats

hyper_res <- cdsrgsea::run_hyper(nutlin,gene_sets$Hallmark,gene_var = "Gene",
                                 rank_var = "logFC",dir = "pos",n_genes = 100)
hyper_res

run_gsea

run_gsea runs gene set enrichment analysis using the fgseaMultilevel method from the fgsea package. The function excepts a table with gene level stats. The dir parameter indicates whether to return positive gene sets, negative gene sets, or both.

gsea_res <- cdsrgsea::run_gsea(nutlin,gene_sets$Hallmark,gene_var = "Gene",
                               rank_var = "logFC",dir = "both")
gsea_res

Plot results

This package is designed to be used with the plotting functions in cdsr_plots

make_gsea_bar

cdsrplots::make_gsea_bar(hyper_res,dir = "pos")

make_gsea_dot

cdsrplots::make_gsea_dot(gsea_res,dir = "both")

broadinstitute/cdsr_gsea documentation built on Sept. 1, 2020, 5:39 a.m.