Man pages for TFEA.ChIP
Analyze Transcription Factor Enrichment
| 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... |
| Genes.Upreg | List of Entrez Gene IDs |
| get_chip_index | Creates df containing accessions of ChIP-Seq datasets and TF. |
| getCMstats | Generate statistical parameters from a contingency_matrix... |
| get_LFC_bar | Plots a color bar from log2(Fold Change) values. |
| GR2tfbs_db | Makes a TFBS-gene binding database |
| gr.list | List of one ChIP-Seq dataset |
| GSEA_EnrichmentScore | Computes the weighted GSEA score of gene.set in gene.list. |
| GSEA_ESpermutations | Calculate enrichment scores for a permutation test. |
| GSEA.result | Output of the function GSEA.run from the TFEA.ChIP package |
| 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... |
| tfbs.database | TFBS database for 3 ChIP-Seq datasets. |
| txt2GR | Function to filter a ChIP-Seq input. |
