MotifMatcher-class: Create a MotifMatcher object

In PriceLab/trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Create a MotifMatcher object

Description

A MotifMatcher object is used directly by the HumanDHSFilter class to match motif matrices to where they occur in the supplied genome.

The MotifMatcher class is used to match motif position weight matrices to places where they occur in a given genome. It requries specification of a genome to search in and a list of motifs to search for. Ordinarily this class is primarily used by the HumanDHSFilter, but can alternatively be used to search for motifs in a given genome without any filtering functionality.

Usage

MotifMatcher(genomeName, pfms, quiet = TRUE)

Arguments

genomeName	A character string identifying an object of type BSgenome. The genome object contains the information for a specific human genome and should be either "hg38" or "hg19". The supplied genome serves as the search space for matching motifs (default = "hg38").
pfms	A list of motif matrices to serve as queries for the target genome. If supplied, these should be created using a MotifList object from the MotifDb package (see example below). If unspecified, the motifs will default to all vertebrates in the JASPAR database (default = list())
quiet	A logical denoting whether or not the MotifMatcher object should print output

Value

An object of the MotifMatcher class

See Also

HumanDHSFilter

Examples

# Specify the genome, and motif list to create a MotifMatcher for only human motifs
library(MotifDb)
mm <- MotifMatcher( genomeName="hg38",
pfms = as.list(query(MotifDb, "sapiens")))

PriceLab/trena documentation built on March 16, 2023, 10:01 a.m.