Analyze Transcription Factor Enrichment

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Documentation for package ‘TFEA.ChIP’ version 1.8.0

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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_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
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.
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.
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.