check_sd: Check gene-wise STD of each one matrix

In hui-sheen/MetaGSCA: Meta-analysis of Gene Set differential Co-expression Analysis

Check gene-wise STD of each one matrix

Description

Check if data matrix per group has a minimum or higher per-gene STD

Usage

check_sd(objt1, objt2, genes, min.sd = 0.001)

Arguments

objt1	dataset for condition 1, genes in columns
objt2	dataset for condition 2, genes in columns
genes	gene names or colnames of objt1/objt2
min.sd	a valid data matrix per group must have at least this much per-feature STD

Value

list of retained genes and to-be-removed genes for STD reason

Examples

data(meta)
STAD <- datasets[['STAD']]
N <- ncol(STAD)
n1 <- N%/%2
objt1 <- t(STAD[,1:n1])
objt2 <- t(STAD[,(n1+1):N])
genes <- rownames(STAD)
check.res <- check_sd(objt1,objt2,genes,0.1)

hui-sheen/MetaGSCA documentation built on April 9, 2022, 7:24 p.m.