t_choose: t_choose

In tinyarray: Expression Data Analysis and Visualization

t_choose

Description

choose differential expressed genes by simple t.test

Usage

t_choose(
  genes,
  exp,
  group_list,
  up_only = FALSE,
  down_only = FALSE,
  pvalue_cutoff = 0.05
)

Arguments

genes	a vector with some genes
exp	A numeric matrix
group_list	A factor with duplicated character or factor
up_only	keep up genes in the result only
down_only	keep down genes in the result only
pvalue_cutoff	p value cut off ,0.05 by defult

Value

a vector with differential expressed genes

Author(s)

Xiaojie Sun

Examples

exp = matrix(rnorm(1000),ncol = 10)
rownames(exp) = sample(mRNA_annov23$gene_id,100)
colnames(exp) = c(paste0("TCGA",1:5),paste0("GTEX",1:5))
exp2  = trans_exp(exp)
exp2[,1:5] = exp2[,1:5]+10
group_list = rep(c("A","B"),each = 5)
genes = sample(rownames(exp2),3)
t_choose(genes,exp2,group_list)

tinyarray documentation built on Aug. 18, 2023, 9:07 a.m.