TFutils


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Documentation for package ‘TFutils’ version 1.4.0

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"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