TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment

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Documentation for package ‘TFEA.ChIP’ version 1.29.2

• 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.