1. MotifDb
  2. man
  3. associateTranscriptionFactors.Rd
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big speedup of associateTranscriptionFactors method, exploiting duplicate motifs

paul-shannon authored on 18/10/2018 14:18:37
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man/associateTranscriptionFactors.Rd
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 }
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 \usage{
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-\S4method{associateTranscriptionFactors}{MotifList}(object, tbl.withMotifs, source, expand.rows)
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+\S4method{associateTranscriptionFactors}{MotifList}(object, tbl.withMotifs, source, expand.rows, motifColumnName="motifName")
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 }
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 \arguments{
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   \item{object}{a \code{MotifList} object.}
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   \item{tbl.withMotifs}{a \code{data.frame}}
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-  \item{source}{a \code{character} string, either 'MotifDb' or "TFClass' (case insensitive)}
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-    \item{expand.rows}{a \code{logical} value, recommended especially for the TFClass source,
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-      in which sometimes many TFs are mapped to the same motif}
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+  \item{source}{a \code{character} string, either "MotifDb" or "TFClass" (case insensitive)}
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+  \item{expand.rows}{a \code{logical} value, recommended especially for the TFClass source,
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+    in which sometimes many TFs are mapped to the same motif}
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+  \item{motifColumnName}{a \code{character} string identifying the
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+    column in tbl.withMotifs which contains the motifs to be associated
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+    with transcription factors}
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 }
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 \value{
Browse code

documentation for geneToMotif, motifToGene, associateT...

paul-shannon authored on 04/10/2017 19:49:25
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man/associateTranscriptionFactors.Rd
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+\name{associateTranscriptionFactors}
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+\alias{associateTranscriptionFactors,MotifList-method}
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+\alias{associateTranscriptionFactors}
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+\title{associateTranscriptionFactors}
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+\description{
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+In the analysis of, or exploration of gene regulatory networks, one
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+often creates a data.frame of possible genomic regulatory sites, genomic
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+locations where a TF binding motif matches some DNA sequence.  A common
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+next step is to associate each of these motifs with its related
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+transcription factor/s.     We provide two sources for those
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+relationships.  When you specify the "MotifDb" source, we return
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+the motif/TF relationships provided by each of the constituent
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+public MotifDb sources.  When you specify the "TFClass" source,
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+transcription factor family memberships (described in
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+\url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383905/}) are -
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+sometimes expansively - provided for each motif you supply.
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+
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+This method uses, and therefore expects, different columns of the incoming data.frame
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+to be used with each method.  The MotifDb source uses the "motifName" column of
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+the incoming data.frame.  The TFClass source expects a "shortName"
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+column in the incoming database.
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+
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+A new column, "geneSymbol", is added to the incoming data.frame.  This
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+new column identifies the transcription factor associated with the motif
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+for each row in the data.frame.
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+
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+}
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+\usage{
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+\S4method{associateTranscriptionFactors}{MotifList}(object, tbl.withMotifs, source, expand.rows)
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+}
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+\arguments{
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+  \item{object}{a \code{MotifList} object.}
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+  \item{tbl.withMotifs}{a \code{data.frame}}
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+  \item{source}{a \code{character} string, either 'MotifDb' or "TFClass' (case insensitive)}
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+    \item{expand.rows}{a \code{logical} value, recommended especially for the TFClass source,
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+      in which sometimes many TFs are mapped to the same motif}
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+}
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+
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+\value{
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+  A data.frame with one column ("geneSymbol") and possibly multiple rows added
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+}
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+\author{Paul Shannon}
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+
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+\examples{
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+  tbl.tfClassExample <- data.frame(motifName=c("MA0006.1", "MA0042.2", "MA0043.2"),
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+                                   chrom=c("chr1", "chr1", "chr1"),
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+                                   start=c(1000005, 1000085, 1000105),
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+                                   start=c(1000013, 1000092, 1000123),
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+                                   score=c(0.85, 0.92, 0.98),
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+                                   stringsAsFactors=FALSE)
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+      # here we illustrate how to add a column with the required name:
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+  tbl.tfClassExample$shortMotif <- tbl.tfClassExample$motifName
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+  tbl.out <- associateTranscriptionFactors(MotifDb, tbl.tfClassExample, source="TFClass",
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+                                           expand.rows=TRUE)
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+  dim(tbl.out)   #    MANY tfs mapped, mostly FOX family genes
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+  tbl.motifDbExample <- data.frame(motifName=c("Mmusculus-jaspar2016-Ahr::Arnt-MA0006.1",
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+                                               "Hsapiens-jaspar2016-FOXI1-MA0042.2",
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+                                               "Hsapiens-jaspar2016-HLF-MA0043.2"),
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+                                    chrom=c("chr1", "chr1", "chr1"),
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+                                    start=c(1000005, 1000085, 1000105),
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+                                    start=c(1000013, 1000092, 1000123),
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+                                    score=c(0.85, 0.92, 0.98),
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+                                    stringsAsFactors=FALSE)
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+
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+   tbl.out <- associateTranscriptionFactors(MotifDb, tbl.motifDbExample, source="MotifDb",
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+                                            expand.rows=TRUE)
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+   dim(tbl.out)   # one new column ("geneSymbol"), no new rows
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+}
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+\seealso{
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+  MotifDb,
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+  geneToMotif,
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+  motifToGene,
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+  subset,
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+  query
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+}
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+
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+\keyword{utilities}