Analyze Transcription Factor Enrichment

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Documentation for package ‘TFEA.ChIP’ version 1.29.0

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

Help Pages

ARNT.metadata	Metadata data frame
ARNT.peaks.bed	ChIP-Seq dataset
ChIPDB	TF-gene binding binary 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
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 certain transcription factors in a plotly graph.
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
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.
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.
txt2GR	Function to filter a ChIP-Seq input.