TFutils


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Documentation for package ‘TFutils’ version 1.0.0

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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
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
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
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
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
URL_s3_tf utility to generate link to biocfound bucket for FIMO TFBS scores