filter_motifs {universalmotif} | R Documentation

## Filter a list of motifs.

### Description

Filter motifs based on the contents of available universalmotif slots. If the input motifs are not of universalmotif, then they they will be converted for the duration of the `filter_motifs()` operation.

### Usage

    filter_motifs(motifs, name, altname, family, organism, width, alphabet,
      type, icscore, nsites, strand, pval, qval, eval)

### Arguments

`motifs` | `list` See `convert_motifs()` for acceptable formats.
`name` | `character` Keep motifs by names.
`altname` | `character` Keep motifs by altnames.
`family` | `character` Keep motifs by family.
`organism` | `character` Keep motifs by organism.
`width` | `numeric(1)` Keep motifs with minimum width.
`alphabet` | `character` Keep motifs by alphabet.
`type` | `character` Keep motifs by type.
`icscore` | `numeric(1)` Keep motifs with minimum total IC.
`nsites` | `numeric(1)` Keep motifs with minimum number of target sites.
`strand` | `character` Keeps motifs by strand.
`pval` | `numeric(1)` Keep motifs by max P-value.
`qval` | `numeric(1)` Keep motifs by max Q-value.
`eval` | `numeric(1)` Keep motifs by max E-val.

### Value

`list` Motifs. An attempt will be made to preserve the original class, see `convert_motifs()` for limitations.

### Author(s)

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

### Examples

    ## By minimum IC:
    jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                      package = "universalmotif"))
    jaspar.ic10 <- filter_motifs(jaspar, icscore = 10)

    ## By organism:
    if (requireNamespace("MotifDb", quietly = TRUE) && .Platform$OS.type == "unix") {
      library(MotifDb)
      motifs <- convert_motifs(MotifDb)
      motifs <- filter_motifs(motifs, organism = c("Athaliana", "Mmusculus"))
    }

[Package universalmotif version 1.0.22 Index]