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decode (version 1.0)

Differential Co-expression and Differential Expression Analysis

Description

Given a set of gene expression data and functional gene set data, the program will return a table summary of the selected gene sets with high differential co-expression and high differential expression (HDC-HDE).

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Version

Install

install.packages('decode')

Monthly Downloads

185

Version

1.0

License

GPL-3

Maintainer

Thomas Lui

Last Published

January 28th, 2015

Functions in decode (1.0)

getDE_DC_OptimalThreshold

Perform chi-square optimization
openFileToWrite

Open file to write result
getBonferroniPValue

Adjust p-value by Bonferroni correction
getBestAssociatedGeneSet

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

read functional gene sets
getAssoGeneSetPValue

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

Get gene index of 8 partitions for gene i
sumResult_MinGain

Summarize the functional gene set results into text file
getFDR

Adjust p-value by Benjamini and Hochberg method
runDecode

Differential Co-expression and Differential Expression Analysis