Package 'TFutils'

Description

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

Usage

anchor_pmids(dataframe)

Arguments

Value

data.frame with HTML anchors to pubmed.gov inserted where 7- or 8-digit numbers are found

Note

The method of isolating putative PMIDs is peculiar to patterns found in the comment fields of annotated TF table (supplemental table S1 found in https://www.cell.com/cms/10.1016/j.cell.2018.01.029/attachment/88c0eca1-66f9-4068-b02e-bd3d55144f79/mmc2.xlsx of PMID 29425488). When DT::datatable is called on the output of this function with escape=FALSE the PMIDs will render as hyperlinks. Note that column 1 is assumed to be an ENSEMBL ID which could have 7 or 8 digits but is handled differently

Examples

litdf = data.frame(id="ENSG00000116819", a="Binds the same GCCTGAGGC sequence as the other AP-2s (PMID: 24789576)",
     stringsAsFactors=FALSE)
anchor_pmids(litdf)

Description

use DT::datatable to browse the GO catalogue of human DNA-binding transcription factors in Table S1.A of Lovering et al.

Usage

browse_gotf_main(cache = BiocFileCache::BiocFileCache(ask = FALSE))

Arguments

Value

result of DT::datatable

Examples

if (interactive()) browse_gotf_main()

Description

use DT::datatable to browse the Lambert's Human Transcription Factors repository

Usage

browse_humantfs_main(cache = BiocFileCache::BiocFileCache(ask = FALSE))

Arguments

Value

result of DT::datatable

Examples

if (interactive()) browse_humantfs_main()

Description

browse several hundred disease-TF associations with hyperlinked PMIDs

Usage

browse_lambert_gwaslinks()

Value

DT::datatable

Note

Based on supplemental table S4 of PMID 29425488

Examples

if (interactive()) browse_lambert_gwaslinks()

Description

use DT::datatable to browse the Lambert table S1

Usage

browse_lambert_main(cache = BiocFileCache::BiocFileCache(ask = FALSE))

Arguments

Value

result of DT::datatable

Note

PMIDs are converted to HTML anchors and DT::datatable is run with escape=FALSE.

Examples

if (interactive()) browse_lambert_main()

Description

Update Oct 18 2021

Usage

ccbr_cell_url()

Description

cisbpTFcat: data.frame with information on CISBP TFs for human, retained for reproducibility support; see cisbpTFcat_2.0 for a more recent catalog

Usage

cisbpTFcat

Format

data.frame

Note

Extracted March 2018, checked August 2018. The only changes observed are that genes ZUFSP and T are used has HGNC values in the March catalog; these symbols seem to be absent from the org.Hs.eg.db of August 2018. The records involved are 1356, 7412 and 7413. These symbols were left in the package image of CISBP in August 2018.

Source

http://cisbp.ccbr.utoronto.ca/bulk.php select Homo_sapiens

Examples

head(TFutils::cisbpTFcat)

Description

cisbpTFcat_2.0: data.frame with information on CISBP TFs for human, described in PMID 31133749

Usage

cisbpTFcat_2.0

Format

data.frame

Note

Extracted August 2019.

Source

http://cisbp.ccbr.utoronto.ca/bulk.php select Homo_sapiens

Examples

head(TFutils::cisbpTFcat_2.0)

Description

basic layout parameters for circos

Usage

defaultCircosParms()

Value

a list

Examples

head(defaultCircosParms())

Description

a list of GRanges instances with TF FIMO scores returned by fimo_granges

Usage

demo_fimo_granges

Format

a list of GRanges instances

Examples

names(S4Vectors::mcols(demo_fimo_granges$VDR[[1]]))

Description

demonstrate interoperation of TF catalog with GWAS catalog

Usage

directHitsInCISBP(traitTag, gwascat)

Arguments

Value

data.frame

Examples

data(gwascat_hg19_chr17)
directHitsInCISBP("Prostate cancer" , gwascat_hg19_chr17)

Description

encode690: DataFrame extending AnnotationHub metadata about ENCODE cell line x TF ranges

Usage

encode690

Format

DataFrame

Source

see metadata(encode690)

Examples

names(TFutils::encode690)
TFutils::encode690[,1:5]

Description

create a list of GRanges for FIMO hits in a GenomicFiles instance, corresponding to a GRanges-based query

Usage

fimo_granges(gf, query)

Arguments

Value

a list of GRanges, produced by GenomicFiles::reduceByRange

Note

Be sure to use ⁠register([BPPARAM])⁠ appropriately.

Examples

if (interactive()) {   # need internet
 # setup -- annotate fimo16 object and create an informative
 # query
 colnames(fimo16) = fimo16$HGNC
 si = GenomeInfoDb::Seqinfo(genome="hg19")["chr17"] # to fix query genome
 myg = GRanges("chr17", IRanges(38.07e6,38.09e6), seqinfo=si)
 requireNamespace("BiocParallel")
 BiocParallel::register(BiocParallel::SerialParam())
 f1 = fimo_granges(fimo16[, c("VDR", "POU2F1")], myg)
 f1
}

Description

fimo16: GenomicFiles instance to AWS S3-resident FIMO bed for 16 TFs

Usage

fimo16

Format

GenomicFiles for a TabixFileList

Source

K. Glass FIMO runs, see https://doi.org/10.1016/j.celrep.2017.10.001

Examples

TFutils::fimo16

Description

fimoMap: table with Mnnnn (motif PWM tags) and HGNC symbols for TFs

Usage

fimoMap

Format

data.frame

Source

Kimberly Glass ([email protected])

Examples

head(TFutils::fimoMap)

Description

use EnsDb to generate an exon-level model of genes identified by symbol

Usage

genemodelDF(sym, resource, columnsKept = c("gene_id", "tx_id"), ...)

Arguments

Value

data.frame instance with exons in rows

Note

There are many approaches available to acquiring 'gene models' in Bioconductor; this one emphasizes the use of the exons method for Ensembl annotation.

Examples

if (requireNamespace("EnsDb.Hsapiens.v75")) {
 orm = genemodelDF("ORMDL3", EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75)
 dim(orm)
}
head(orm)

Description

create a GeneRegionTrack instance for selected symbols

Usage

genemodForGviz(
  sym = "ORMDL3",
  id_elem = c("symbol", "tx_id"),
  resource = EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75,
  ...
)

Arguments

Value

instance of Gviz GeneRegionTrack

Note

This function helps to display the locations of TF binding sites in the context of complex gene models. A complication is that we have nice visualization of quantitative affinity predictions for TFs in the vignette, based on ggplot2, but it is not clear how to use that specific code to work with Gviz.

Examples

if (requireNamespace("EnsDb.Hsapiens.v75") &
    requireNamespace("Gviz")) {
 orm = genemodForGviz("ORMDL3", resource= EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75)
 orm
 Gviz::plotTracks(orm, showId=TRUE) # change id_elem for shorter id string
}

Description

utility to obtain location etc. for rsids of SNPs

Usage

get_rslocs_38(rsids = c("rs6060535", "rs56116432"))

Arguments

Value

GRanges instance

Note

Uses rest.ensembl.org, posting to variant_recorder/homo_sapiens. Parses result minimally, using only the first SPDI to obtain location information, adding 1 as ensembl genomic coordinates are zero-based.

Examples

if (interactive()) get_rslocs_38() # see https://stat.ethz.ch/pipermail/bioc-devel/2020-October/017263.html

Description

Update Oct 18 2021

Usage

gotf_url()

Description

create table of TF targets and related metadata

Usage

grabTab(
  tfstub = "STAT1",
  gscoll = TFutils::tftColl,
  orgdb = org.Hs.eg.db::org.Hs.eg.db,
  gwrngs = TFutils::gwascat_hg19_chr17
)

Arguments

Value

data.frame instance

Note

This function will link together information on targets of a given TF to the GWAS catalog.

Examples

gt = grabTab("VDR", gscoll=TFutils::tftColl,
   orgdb=org.Hs.eg.db::org.Hs.eg.db, gwrngs=TFutils::gwascat_hg19_chr17)
dim(gt)
head(gt)

Description

gwascat_hg19: GRanges of march 21 2018 EBI gwascat, limit to chr17

Usage

gwascat_hg19_chr17

Format

GenomicRanges GRanges instance

Source

gwascat::makeCurrentGwascat, with gwascat:::lo38to19 applied

Examples

TFutils::gwascat_hg19_chr17[,1:5]

Description

simple accessor for HGNCmap component of TFCatalog

Usage

HGNCmap(x)

Arguments

Value

dataframe instance

Examples

HGNCmap

Description

hocomoco.mono: data.frame with information on HOCOMOCO TFs for human

Usage

hocomoco.mono

Format

data.frame

Note

Extracted March 2018

Source

http://hocomoco11.autosome.ru/human/mono?full=true

Examples

head(TFutils::hocomoco.mono)

Description

hocomoco.mono.sep2018: data.frame with information on HOCOMOCO TFs for human, Sept 2018 download

Usage

hocomoco.mono.sep2018

Format

data.frame

Note

Extracted September 2018

Source

http://hocomoco11.autosome.ru/human/mono?full=true

Examples

head(TFutils::hocomoco.mono.sep2018)

Description

utility to read FIMO outputs from local resource(cluster), assuming bed text split by chromosome

Usage

importFIMO_local_split(tf, chr)

Arguments

Value

data.table instance

Examples

requireNamespace("GenomicRanges")
requireNamespace("IRanges")
importFIMO_local_split("M5946_1", "chr1")
dim(importFIMO_local_split("M5946_1", "chr17"))

Description

import a FIMO bed-like file

Usage

## S4 method for signature 'TabixFile,GRanges'
importFIMO(src, parms, ...)

## S4 method for signature 'character,missing'
importFIMO(src, parms, ...)

Arguments

Value

instance of GRanges

Examples

if (requireNamespace("Rsamtools")) {
 tf = Rsamtools::TabixFile(system.file("M5946_1/chr1.bed.gz", package="TFutils"))
 importFIMO(tf, GenomicRanges::GRanges("chr1", IRanges::IRanges(1e6,11e6)))
 }

Description

lambert_snps is Table S3 of Lambert et al PMID 29425488

Usage

lambert_snps

Format

data.frame

Examples

head(lambert_snps)

Description

metadata_tf: list with metadata (motif_if and hgnc_symbol) about all the CISBP FIMO scan TF bed files

Usage

metadata_tf

Format

list

Source

K. Glass ran FIMO

Examples

TFutils::metadata_tf

Description

named_tf: named list with the names being the hgnc_symbol of the motif_id

Usage

named_tf

Format

list

Source

K. Glass ran FIMO

Examples

TFutils::named_tf
named_tf[["VDR"]]

Description

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

Usage

retrieve_gotf_main(cache = BiocFileCache::BiocFileCache(ask = FALSE))

Arguments

Value

a tbl_df

Note

This will download the spreadsheet if not found in cache.

Examples

if (interactive()) retrieve_gotf_main()

Description

acquire the CSV content for table S1 of Lambert et al. Cell 2018 from the Human TFS repository at http://humantfs.ccbr.utoronto.ca

Usage

retrieve_humantfs_main(cache = BiocFileCache::BiocFileCache(ask = FALSE))

Arguments

Value

a tbl_df

Note

This will download the spreadsheet if not found in cache.

Examples

if (interactive()) retrieve_humantfs_main()

Description

acquire the Excel spreadsheet content for table S1 of Lambert et al. Cell 2018, "The Human Transcription Factors"

Usage

retrieve_lambert_main(cache = BiocFileCache::BiocFileCache(ask = FALSE))

Arguments

Value

a tbl_df

Note

This will download the spreadsheet if not found in cache.

Examples

if (interactive()) retrieve_lambert_main()

Description

a Seqinfo instance for a chr17 in hg19

Usage

seqinfo_hg19_chr17

Format

a Seqinfo instance

Examples

seqinfo_hg19_chr17

Description

process a gene_attribute_matrix.txt file from harmonizeome into a GeneSetCollection

Usage

setupHIZE(txtfn = "gene_attribute_matrix.txt", tag)

Arguments

Value

GSEABase::GeneSetCollection

Note

After uncompressing content of http://amp.pharm.mssm.edu/static/hdfs/harmonizome/data/cheappi/gene_attribute_matrix.txt.gz run this on gene_attribute_matrix.txt with tag="CHEA".

Description

produce a concise report on TFCatalog instance

Usage

## S4 method for signature 'TFCatalog'
show(object)

Arguments

Value

side effect

Description

Constructor for TFCatalog

Usage

TFCatalog(name, nativeIds, HGNCmap, metadata)

Arguments

Value

instance of TFCatalog

Examples

if (require("GSEABase")) {
 TFs_MSIG = TFCatalog(name="MsigDb.TFT",nativeIds=names(TFutils::tftColl),
 HGNCmap=data.frame(TFutils::tftCollMap,stringAsFactors=FALSE))
 TFs_MSIG
}

Description

define a structure to hold information about TFs from diverse reference sources

Slots

name

character

nativeIds

character tokens used by the provider to enumerate transcription factors

HGNCmap

data.frame with atleast two columns, native id as first column and HGNC symbol as second column

metadata

ANY

Note

This class respects the notions that 1) a source of information about transcription factors should have a name, 2) each source has its own 'native' nomenclature for the factors themselves, 3) it is common to use the gene symbol to refer to the transctiption factor, and 4) additional metadata will frequently be required to establish information about provenance of assertions about transcription factors.

Description

use a radial plot (by default) for motif stack

Usage

tffamCirc.plot(motiflist, circosParms = defaultCircosParms())

Arguments

Value

side effect to graphics device

Examples

p1 = tffamCirc.prep( )
tffamCirc.plot(p1[c(1:8, 10:17, 19)])

Description

set up list of pfms in motifStack protocol

Usage

tffamCirc.prep(tffam = "Paired-related HD factors{3.1.3}", trimfac = 0.4)

Arguments

Value

a list of pfm instances as defined in motifStack

Note

Uses MotifDb, motifStack to create a list of pfms

Examples

n1 = tffamCirc.prep()
str(n1)

Description

tfhash: data.frame with MSigDb TFs, TF targets as symbol or ENTREZ

Usage

tfhash

Format

list

Source

MSigDb "c3" (motif gene sets) has been harvested for simple annotation of TFs and targets.

Examples

TFutils::tfhash
tfhash[1:3,]

Description

gadget to help sort through tags naming TFs

Usage

TFtargs(
  gscoll = TFutils::tftColl,
  initTF = "VDR_Q3",
  gwcat = TFutils::gwascat_hg19_chr17,
  gadtitle =
    "Search for a TF; its targets will be checked for mapped status in GWAS catalog"
)

Arguments

Value

on app conclusion a data.frame is returned

Note

Will use TFutils::gwascat_hg19_chr17 to look for 'MAPPED_GENE' field entries matching targets, also hardcoded to use org.Hs.eg.db to map symbols

Examples

if (interactive()) TFtargs()

Description

tftColl: GSEABase GeneSetCollection for transcription factor targets

Usage

tftColl

Format

GSEABase GeneSetCollection instance

Note

run GSEABase::getGMT() on c3/TFT geneset collection from MSigDb

Source

broad institute

Examples

TFutils::tftColl

Description

tftCollMap: data.frame with information on MSigDb TFs for human

Usage

tftCollMap

Format

data.frame

Note

Annotation of TFs is ad-hoc. GeneSet names were tokenized, splitting by underscore, and then fragments were matched to SYMBOL and ALIAS elements of org.Hs.eg.db. Extracted March 2018

Source

http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=TFT

Examples

head(TFutils::tftCollMap)

Description

Use MSigDB TF targets resource to find targets of input TF and find traits to which these targets have been mapped

Usage

topTraitsOfTargets(TFsym, gsc, gwcat, ntraits = 6, force = FALSE, ...)

Arguments

Value

data.frame symbol, set force = TRUE to use a known 'motif' name among names(gsc)

Note

If tftCollMap[, "hgnc.heur"] does not possess the necessary

Examples

suppressPackageStartupMessages({
library(GSEABase)
})  # more results if you substitute ebicat37 from gwascat below
topTraitsOfTargets("MTF1" , tftColl, gwascat_hg19_chr17)

Description

utility to generate link to biocfound bucket for FIMO TFBS scores

Usage

URL_s3_tf(tag = "M3433")

Arguments

Value

character(1) URL

Examples

URL_s3_tf