# TFutils

## Documentation for package ‘TFutils’ version 1.4.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

"TFCatalog-class" | define a structure to hold information about TFs from diverse reference sources
cisbpTFcat | cisbpTFcat: data.frame with information on CISBP TFs for human
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
genemodelDF | use EnsDb to generate an exon-level model of genes identified by symbol
genemodForGviz | create a GeneRegionTrack instance for selected symbols
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@importFrom utils read.delim
importFIMO-method | import a FIMO bed-like file@importFrom utils read.delim
importFIMO_local_split | utility to read FIMO outputs from local resource(cluster), assuming bed text split by chromosome
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
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
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