mCut: provide cutoff threshold and gene expression values for...

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

provide cutoff threshold and gene expression values for specific gene

Description

provide cutoff threshold and gene expression values for specific gene

Usage

mCut(gene, mat, os, cut = "median")

Arguments

gene	the gene we want to use to classify samples based on expression
mat	expression values (FPKM) tibble with samples as columns and symbol column containing gene names
os	tibble with samples, overall survival (OS) values, and Vital.Status values
cut	method to use to separate into high and low groups, can be either median (defualt) or cutP

Value

the cutoff threshold and expression values (log2(FPKM+1)) as a list

Examples

data = abs(data.frame(data = matrix(rnorm(100),ncol=10)))
expr = dplyr::tibble(symbol = paste0(rep("gene",10),1:10), data)
colnames(expr) = c("symbol", letters[1:10])
os = dplyr::tibble(sample = letters[1:10], OS = 10:19, Vital.Status = c(rep("Alive",8),rep("Dead",2)))
mCut("gene1", mat = expr, os = os, cut = "cutP")

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