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decode (version 1.1)

Differential Co-Expression and Differential Expression Analysis

Description

Integrated differential expression (DE) and differential co-expression (DC) analysis on gene expression data based on DECODE (DifferEntial CO-expression and Differential Expression) algorithm.

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Version

Install

install.packages('decode')

Monthly Downloads

185

Version

1.1

License

GPL-3

Maintainer

Thomas Lui

Last Published

March 18th, 2015

Functions in decode (1.1)

getAssoGeneSetPValue

Calculate the p-value between selected genes and functional gene set
getPartitionIndex

Get gene index of 8 partitions for gene i
getPathway

read functional gene sets
getFDR

Adjust p-value by Benjamini and Hochberg method
runDecode

Differential Co-Expression and Differential Expression Analysis
openFileToWrite

Open file to write result
getDE_DC_OptimalThreshold

Perform chi-square optimization
getBestAssociatedGeneSet

Get best associated functional gene sets for partitions of gene i
getBonferroniPValue

Adjust p-value by Bonferroni correction
sumResult_MinGain

Summarize the functional gene set results into text file