Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data

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Documentation for package ‘DCGL’ version 2.1.2

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DCGL-package Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data
ASC Identify DCGs (Differential Coexpressed Genes) based on 'Average Specific Connection'
DCe Identify DCGs (Differentially Coexpressed Genes) and DCLs (Differentially Coexpressed Links)
DCGL Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data
DCp Identify DCGs (Differential Coexpressed Genes) based on the 'Differential Coexpression Profile'
DCsum Summarize DCGs and DCLs
DRplot Visualization of DRLs
DRrank Ranking Regulators by Target Enrichment Density (TED) and Targets' DCL Density (TDD)
DRsort Identify DRGs (Differential regulated Genes) and DRLs (Differential regulated Links)
expressionBasedfilter Filter genes according to expression level
exprs Real dataset pulled down from GEO (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17967)
exprs_design Experiment design of microarray matrix data
intgenelist Interesting genes list
LFC Select DCLs based on 'Limit Fold Change' model
LRC Identify DCGs (Differential Coexpressed genes) based on 'Log Ratio Connections'
percentLinkfilter Filter gene coexpression links according to the top percent of expression correlation coefficient value
qLinkfilter Filter gene coexpression links according to the q-values of expression correlation values
RIF Ranking Regulators by Regulator Impact Factor (RIF) Method
rLinkfilter Filter gene coexpression links according to correlation coefficient value
tf2target The dataset of human Transcription Factors regulate potential target genes
varianceBasedfilter To filter genes according to expression variability
WGCNA Identify DCGs (Differential Coexpressed Genes) based on the 'Weighted Gene Coexpression Network Analysis'