importAme: Parse AME output

In snystrom/memes: motif matching, comparison, and de novo discovery using the MEME Suite

Parse AME output

Description

This imports AME results using the "ame.tsv" output, and optionally the "sequences.tsv" output if run with "method = fisher". AME results differ based on the method used, thus this must be set on import or the column names will be incorrect.

Usage

importAme(
  path,
  method = c("fisher", "ranksum", "dmhg3", "dmhg4", "pearson", "spearman"),
  sequences = NULL
)

Arguments

path	path to ame results file ("ame.tsv")
method	ame run method used (one of: c("fisher", "ranksum", "dmhg3", "dmhg4", "pearson", "spearman")). Default: "fisher".
sequences	NULL/FALSE to skip sequence import, or path to sequences file to import (only valid for method = "fisher")

Value

data.frame with method-specific results. See [AME results](http://meme-suite.org/doc/ame-output-format.html) webpage for more information. If sequences is set to a path to the sequences.tsv and method = "fisher", the list-column 'sequences' will be appended to resulting data.frame.

See Also

[runAme()]

Examples

ame_tsv <- system.file("extdata", "ame.tsv", package = "memes", mustWork = TRUE)
importAme(ame_tsv)

snystrom/memes documentation built on Oct. 12, 2024, 2:42 a.m.