Differential Co-Expression and Differential Expression Analysis


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Documentation for package ‘decode’ version 1.2

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