Differential Co-Expression and Differential Expression Analysis

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Documentation for package ‘decode’ version 1.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

getAssoGeneSetPValue	Calculate the p-value between selected genes and functional gene set
getBestAssociatedGeneSet	Get best associated functional gene sets for partitions of gene i
getBonferroniPValue	Adjust p-value by Bonferroni correction
getDE_DC_OptimalThreshold	Perform chi-square optimization
getFDR	Adjust p-value by Benjamini and Hochberg method
getPartitionIndex	Get gene index of 8 partitions for gene i
getPathway	read functional gene sets
openFileToWrite	Open file to write result
runDecode	Differential Co-Expression and Differential Expression Analysis
sumResult_MinGain	Summarize the functional gene set results into text file