MotifMatcher-class {trena} | R Documentation

## 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")))

[Package trena version 1.12.1 Index]