# TFutils

## Documentation for package ‘TFutils’ version 1.31.0

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

## Help Pages

"TFCatalog-class" | define a structure to hold information about TFs from diverse reference sources
anchor_pmids | check columns of a dataframe for numerical tokens of 7 or 8 digits and create HTML anchors to pubmed.gov constituting a link to a PMID
browse_gotf_main | use DT::datatable to browse the GO catalogue of human DNA-binding transcription factors in Table S1.A of Lovering et al.
browse_humantfs_main | use DT::datatable to browse the Lambert's Human Transcription Factors repository
browse_lambert_gwaslinks | browse several hundred disease-TF associations with hyperlinked PMIDs
browse_lambert_main | use DT::datatable to browse the Lambert table S1
ccbr_cell_url | Update Oct 18 2021
cisbpTFcat | cisbpTFcat: data.frame with information on CISBP TFs for human, retained for reproducibility support; see cisbpTFcat_2.0 for a more recent catalog
cisbpTFcat_2.0 | cisbpTFcat_2.0: data.frame with information on CISBP TFs for human, described in PMID 31133749
defaultCircosParms | basic layout parameters for circos
demo_fimo_granges | a list of GRanges instances with TF FIMO scores returned by 'fimo_granges'
directHitsInCISBP | demonstrate interoperation of TF catalog with GWAS catalog
encode690 | encode690: DataFrame extending AnnotationHub metadata about ENCODE cell line x TF ranges
fimo16 | fimo16: GenomicFiles instance to AWS S3-resident FIMO bed for 16 TFs
fimoMap | fimoMap: table with Mnnnn (motif PWM tags) and HGNC symbols for TFs
fimo_granges | create a list of GRanges for FIMO hits in a GenomicFiles instance, corresponding to a GRanges-based query
genemodelDF | use EnsDb to generate an exon-level model of genes identified by symbol
genemodForGviz | create a GeneRegionTrack instance for selected symbols
get_rslocs_38 | utility to obtain location etc. for rsids of SNPs
gotf_url | Update Oct 18 2021
grabTab | create table of TF targets and related metadata
gwascat_hg19_chr17 | gwascat_hg19: GRanges of march 21 2018 EBI gwascat, limit to chr17
HGNCmap | simple accessor for HGNCmap component of TFCatalog
hocomoco.mono | hocomoco.mono: data.frame with information on HOCOMOCO TFs for human
hocomoco.mono.sep2018 | hocomoco.mono.sep2018: data.frame with information on HOCOMOCO TFs for human, Sept 2018 download
importFIMO | import a FIMO bed-like file
importFIMO-method | import a FIMO bed-like file
importFIMO_local_split | utility to read FIMO outputs from local resource(cluster), assuming bed text split by chromosome
lambert_snps | lambert_snps is Table S3 of Lambert et al PMID 29425488
metadata_tf | metadata_tf: list with metadata (motif_if and hgnc_symbol) about all the CISBP FIMO scan TF bed files
named_tf | named_tf: named list with the names being the hgnc_symbol of the motif_id
retrieve_gotf_main | acquire the content of Table S1.A from Lovering et al., A GO catalogue of human DNA-binding transcription factors, DOI: https://doi.org/10.1101/2020.10.28.359232
retrieve_humantfs_main | acquire the CSV content for table S1 of Lambert et al. Cell 2018 from the Human TFS repository at http://humantfs.ccbr.utoronto.ca
retrieve_lambert_main | acquire the Excel spreadsheet content for table S1 of Lambert et al. Cell 2018, "The Human Transcription Factors"
seqinfo_hg19_chr17 | a Seqinfo instance for a chr17 in hg19
setupHIZE | process a gene_attribute_matrix.txt file from harmonizeome into a GeneSetCollection
show-method | produce a concise report on TFCatalog instance
TFCatalog | Constructor for TFCatalog
TFCatalog-class | define a structure to hold information about TFs from diverse reference sources
tffamCirc.plot | use a radial plot (by default) for motif stack
tffamCirc.prep | set up list of pfms in motifStack protocol
tfhash | tfhash: data.frame with MSigDb TFs, TF targets as symbol or ENTREZ
TFtargs | gadget to help sort through tags naming TFs
tftColl | tftColl: GSEABase GeneSetCollection for transcription factor targets
tftCollMap | tftCollMap: data.frame with information on MSigDb TFs for human
topTraitsOfTargets | Use MSigDB TF targets resource to find targets of input TF and find traits to which these targets have been mapped
URL_s3_tf | utility to generate link to biocfound bucket for FIMO TFBS scores