# Analyze Transcription Factor Enrichment

## Documentation for package ‘TFEA.ChIP’ version 1.0.0

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

## Help Pages

ARNT.metadata | Metadata data frame
ARNT.peaks.bed | ChIP-Seq dataset
CM_list | List of contingency matrix
contingency_matrix | Computes 2x2 contingency matrices
DnaseHS_db | DHS databse
Entrez.gene.IDs | List of Entrez Gene IDs
GeneID2entrez | Translates gene IDs from Gene Symbol or Ensemble ID to Entrez ID.
Genes.Upreg | List of Entrez Gene IDs
getCMstats | Generate statistical parameters from a contingency_matrix output
get_chip_index | Creates df containing accessions of ChIP-Seq datasets and TF.
get_LFC_bar | Plots a color bar from log2(Fold Change) values.
gr.list | List of one ChIP-Seq dataset
GR2tfbs_db | Makes a TFBS-gene binding database
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_run | Function to run a GSEA analysis
GSEA_Shuffling | Function to create shuffled gene lists to run GSEA.
highlight_TF | Highlight certain transcription factors in a plotly graph.
hypoxia | RNA-Seq experiment
hypoxia_DESeq | RNA-Seq experiment
log2.FC | List of Entrez Gene IDs
makeTFBSmatrix | Function to search for a list of entrez gene IDs.
Mat01 | TF-gene binding binary matrix
MetaData | TF-gene binding DB metadata
plot_CM | Makes an interactive html plot from an enrichment table.
plot_ES | Plots Enrichment Score from the output of GSEA.run.
plot_RES | Plots all the RES stored in a GSEA_run output.
preprocessInputData | Extracts data from a DESeqResults object or a data frame.
Select_genes | Extracts genes according to logFoldChange and p-val limits
set_user_data | Sets the data objects as default.
stat_mat | Data frame, output from the function getCMstats from the TFEA.ChIP package
tfbs.database | TFBS database for 3 ChIP-Seq datasets.
txt2GR | Function to filter a ChIP-Seq input.