ccn_makeGRN: make GRN

In pcahan1/cancerCellNet: CellNet, for cancer

make GRN

Description

Construct GRN

Usage

ccn_makeGRN(
  expTrain,
  stTrain,
  dLevel,
  zThresh = 4,
  dLevelGK = NULL,
  prune = FALSE,
  holm = 1e-04,
  cval = 0.4,
  species = "Hs"
)

Arguments

expTrain	normalized expression matrix
stTrain	sample table
dLevel	name of the column with different categories
zThresh	threshold of z score for CLR network reconstruction
dLevelGK	name of the column with different germlayer categories
prune	boolean limit to genes exclusively detected as CT in one CT
holm	threshold of holm adjusted p value for selecting subnetwork genes
cval	threshold of cval for selectin subnetwork genes. Higher cval indicates selecting higher enriched genes
species	Hs or Mm indicating human or mouse

Value

constructed GRN

pcahan1/cancerCellNet documentation built on July 16, 2022, 12:12 a.m.