Run_permutation: Given a diff-reg results, do permutation on group label

In ningb/diffreg: Differential Regulation Analysis of miRNAs

Given a diff-reg results, do permutation on group label

Description

Given a diff-reg results, do permutation on group label

Usage

Run_permutation(
  diffreg.res,
  mrna.mat,
  mirna.mat,
  raw.mrna.mat = NULL,
  raw.mirna.mat = NULL,
  do.spqn = TRUE,
  target.mat,
  group.label,
  do.parallel = FALSE,
  n.iter = 1000,
  seed = 1234
)

Arguments

diffreg.res	Differential regulation results from Run_diffreg()
mrna.mat	A matrix of mRNA expression (genes at rows and samples at columns)
mirna.mat	A matrix of miRNA expression (genes at rows and samples at columns)
raw.mrna.mat	(optional) A raw matrix of mRNA expression (genes at rows and samples at columns)
raw.mirna.mat	(optional) A raw matrix of miRNA expression (genes at rows and samples at columns)
do.spqn	A logical variable indication whether SpQN should be done
target.mat	A binary matrix indicating target with miRNA on columns and mRNA on rows
group.label	A factor vector subtype label for the samples
do.parallel	A logical variable indicating whether parallization will be performed
n.iter	An integer indicating the number of interaions for n.iter
seed	A integer for permutation seed

Value

A data frame similar to output from Run_diffreg() with additional permutation significance values

ningb/diffreg documentation built on Jan. 20, 2025, 4:10 p.m.