TFutils

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Documentation for package ‘TFutils’ version 1.29.0

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

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