dgsea_untargeted: This function performs untargeted DGSEA comparing all gene...

In JamesJoly/DGSEA: Differential Gene Set Enrichment Analysis

Description

This function performs untargeted DGSEA comparing all gene sets to each other

Usage

dgsea_untargeted(
  input.df,
  gmt.list,
  num.permutations = 1000,
  stat.type = "Weighted"
)

Arguments

input.df	Data frame containing Genes in column 1 and ranking metrics for samples (e.g signal-to-noise ratio) in columns 2:N
gmt.list	gmt list containing the gene sets the user wishes to use with gene set name as column name and genes in the rows (i.e. from GSA.read.gmt())
num.permutations	Number of permutations to perform, default = 1000
stat.type	Character string set to "Weighted" (weight = 1) or "Classic" (score weight = 0), default is "Weighted"

Value

A list containing DGSEA results, GSEA results, and information to make mountain plots using the make_mountain_plots function

Examples

expression_data <- seq(-1,1, by = 0.077)
Gene <- LETTERS[seq(from = 1, to = 26)]
data <- as.data.frame(cbind(Gene,expression_data))
gene.set.A <- c("A","B","C","D","E")
gene.set.B <- c("V","W","X","Y","Z")
gene.set.X <- c("J","Q","O","E","F")
gene.set.Y <- c("D","S","K","L","R")
gene.set.Z <- c("G","W","P","B","T")
names <- c("gene.set.A","gene.set.B","gene.set.X","gene.set.Y","gene.set.Z")
Letter.Sets <- list(gene.set.A,gene.set.B,gene.set.X,gene.set.Y,gene.set.Z)
names(Letter.Sets) <- NULL
Gene.Sets <- list(genesets = Letter.Sets, geneset.names = names)

dgsea_untargeted(input.df = data, gmt.list = Gene.Sets)

JamesJoly/DGSEA documentation built on May 23, 2021, 6:32 a.m.