This package implements INDEED algorithm from Zuo et. al.’s Methods paper: INDEED: Integrated differential expression and differential network analysis of omic data for biomarker discovery (PMID: 27592383).
This R package will generate a csv file containing information such as p-values, node degree and activity score for each biomolecule. A higher activity score indicates that the corresponding biomolecule has more neighbors connceted in the differential network and their p-values are more statistically significant. It will also generate a csv file for the differential network created by INDEED.
You can install INDEED from github with:
# The development version from GitHub:
# install.packages("devtools")
devtools::install_github("cx30/INDEED")library(INDEED)
# Example 1:
# Using partial correlation to obtain sparse differential network
select_sig(Met_GU, Met_Group_GU, Met_name_GU, partial = TRUE)
# Example 2:
# Using Spearman correlation to obtain differential network
select_sig(Met_GU, Met_Group_GU, Met_name_GU, partial = FALSE, method = "spearman")