ts.IUT: ts.IUT

In warelab/NECorr: Gene Regulatory Network Correlations

ts.IUT

Description

combine the TSI/TSE test and IUT to determine the tissue specific genes and the tissue excluded genes. list of list with 4 methods raw and filtered results matrix of tissue specific genes for each method; upload all libraries gplots TCC upload function below TissueTransform, DiscNULLrow, factOrg, IUTest, numeratorTSI, denominator, TSI, tsi.matrix, plotlOnegene, plotLfewGenes, heatmap.ts, tindex, tindex.matrix,

Usage

ts.IUT(name = "exp", eset, tissues, target, threshold = 0.05, filter = 50)

Arguments

name	name of the data
eset	matrix of expression data in matrix format in TPM for example but any other expression matrix
tissues	character vector defining the the tissue type of each column present in the expression table
target	the target tissues
threshold	represent the p-value for the IUT test after Sidak correction; the outlier percentage for the ROKU test the percentage of (1 -threshold for the Tindex and the TSI tests)
filter	the minimal expression level for the tissue/condition of interest; the default is set at 100; expression of 100 TPM

Value

list.all csv.table output for each type of analysis will be written in the table folder

warelab/NECorr documentation built on Oct. 15, 2023, 11:31 a.m.