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decode (version 1.2)

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

1.2

License

GPL-3

Maintainer

Thomas Lui

Last Published

July 14th, 2015

Functions in decode (1.2)

getAssoGeneSetPValue

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

Open file to write result
runDecode

Differential Co-Expression and Differential Expression Analysis
getPartitionIndex

Get gene index of 8 partitions for gene i
sumResult_MinGain

Summarize the functional gene set results into text file
getPathway

read functional gene sets
getDE_DC_OptimalThreshold

Perform chi-square optimization
getBonferroniPValue

Adjust p-value by Bonferroni correction
getFDR

Adjust p-value by Benjamini and Hochberg method
getBestAssociatedGeneSet

Get best associated functional gene sets for partitions of gene i