mSet: provide cutoff threshold and GSEA values for gene set of two...

In hmumme/survivalHelp: What the Package Does (One Line, Title Case)

provide cutoff threshold and GSEA values for gene set of two or more genes

Description

provide cutoff threshold and GSEA values for gene set of two or more genes

Usage

mSet(gs, ENS, os, ref, cut = "median")

Arguments

gs	the genes we want to use to classify samples based on expression
ENS	expression values (FPKM) tibble with samples as columns and ENSMBL ids as rows
os	tibble with samples, overall survival (OS) values, and Vital.Status values
ref	reference tibble with ensmble ids and gene symbols as columns, converts to ENS using this
cut	method to use to separate into high and low groups, can be either median (defualt) or cutP

Value

the cutoff threshold and GSEA scores as a list

Examples

expr = abs(matrix(rnorm(100),ncol=10))
rownames(expr) = paste0(rep("ENSG",10),1:10)
colnames(expr) = letters[1:10]
ref = dplyr::tibble(ensg = paste0(rep("ENSG",10), 1:10), symbol = paste0(rep("gene",10), 10:1))
os = dplyr::tibble(sample = letters[1:10], OS = 10:19, Vital.Status = c(rep("Alive",8),rep("Dead",2)))
mSet(c("gene1","gene4","gene5"), ENS = expr, os = os, ref = ref, cut = "cutP")

hmumme/survivalHelp documentation built on June 6, 2022, 9:15 p.m.