# TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment

## Documentation for package ‘TFEA.ChIP’ version 1.31.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

analysis_from_table | Analysis from Input Table
ARNT.metadata | Metadata data frame
ARNT.peaks.bed | ChIP-Seq dataset
ChIPDB | TF-Gene List
chip_metadata | ChIP-seq transcription factor metadata
contingency_matrix | Compute 2x2 Contingency Matrices for ChIP-Seq Enrichment
DnaseHS_db | DHS databse
Entrez.gene.IDs | List of Entrez Gene IDs
filter_expressed_TFs | Filter Expressed TFs
GeneID2entrez | Translates gene IDs from Gene Symbol or Ensembl ID to Entrez ID.
Genes.Upreg | List of Entrez Gene IDs
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
GSEA.result | Output of the function GSEA.run from the TFEA.ChIP package
GSEA_EnrichmentScore | Computes the weighted GSEA score of gene.set in gene.list.
GSEA_ESpermutations | Calculate enrichment scores for a permutation test.
GSEA_run | Function to run a GSEA analysis
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
MetaData | TF-gene binding DB metadata
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'
Select_genes | Extracts genes according to logFoldChange and p-val limits
set_user_data | Sets the data objects as default.
TF_ranking2 | Meta-analysis ranking of transcription factors
txt2GR | Function to filter a ChIP-Seq input.