filter_motifs: Filter a list of motifs.
In bjmt/universalmotif: Import, Modify, and Export Motifs with R

filter_motifs

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 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, extrainfo)

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.
`extrainfo`	`character` Named character vector of items that must be present in motif `extrainfo` slots.

Value

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

Author(s)

Benjamin Jean-Marie Tremblay, benjamin.tremblay@uwaterloo.ca

Examples

## By minimum IC:
jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
jaspar.ic3 <- filter_motifs(jaspar, icscore = 3)

## Starting from version 1.10.0 of the universalmotif package, one
## could instead make use of the universalmotif_df structure:
jaspar.ic3 <- jaspar |> to_df() |> subset(icscore > 3) |> to_list()

## By organism:
## Not run: 
library(MotifDb)
motifs <- convert_motifs(MotifDb)
motifs <- filter_motifs(motifs, organism = c("Athaliana", "Mmusculus"),
                        extrainfo = c("dataSource" = "cisbp_1.02"))
## Or:
motifs <- convert_motifs(MotifDb) |> to_df() |>
  subset(organism %in% c("Athaliana", "Mmusculus") &
    dataSource == "cisbp_1.02") |> to_list()

## End(Not run)

bjmt/universalmotif documentation built on Nov. 16, 2024, 7:38 a.m.