ARNT.metadata           Metadata data frame
ARNT.peaks.bed          ChIP-Seq dataset
ChIPDB                  TF-Gene List
DnaseHS_db              DHS databse
Entrez.gene.IDs         List of Entrez Gene IDs
GSEA.result             Output of the function GSEA.run from the
                        TFEA.ChIP package
GSEA_ESpermutations     Calculate enrichment scores for a permutation
                        test.
GSEA_EnrichmentScore    Computes the weighted GSEA score of gene.set in
                        gene.list.
GSEA_run                Function to run a GSEA analysis
GeneID2entrez           Translates gene IDs from Gene Symbol or Ensembl
                        ID to Entrez ID.
Genes.Upreg             List of Entrez Gene IDs
MetaData                TF-gene binding DB metadata
Select_genes            Extracts genes according to logFoldChange and
                        p-val limits
TF_ranking2             Meta-analysis ranking of transcription factors
analysis_from_table     Analysis from Input Table
chip_metadata           ChIP-seq transcription factor metadata
contingency_matrix      Compute 2x2 Contingency Matrices for ChIP-Seq
                        Enrichment
filter_expressed_TFs    Filter Expressed TFs
getCMstats              Generate statistical parameters from
                        contingency matrices
get_chip_index          Creates df containing accessions of ChIP-Seq
                        datasets and TF.
gr.list                 List of one ChIP-Seq dataset
highlight_TF            Highlight special TFs in enrichment table.
hypoxia                 RNA-Seq experiment
hypoxia_DESeq           RNA-Seq experiment
log2.FC                 List of Entrez Gene IDs
makeChIPGeneDB          Make a ChIP - target database
matrixDB_to_listDB      Re-formatting ChIP-Gene database
metaanalysis_fx         Perform Meta-analysis for each TF
plot_CM                 Interactive HTML Plot for Transcription Factor
                        Enrichment
plot_ES                 Plots Enrichment Score from the output of
                        GSEA.run.
plot_RES                Plot Running Enrichment Scores (RES) and Log2
                        Fold Change (LFC)
preprocessInputData     Extracts data from a DESeqResults object or a
                        data frame.
rankTFs                 Rank the TFs in the output from 'getCMstats'
set_user_data           Sets the data objects as default.
txt2GR                  Function to filter a ChIP-Seq input.
