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

NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")

eval_vignette <- NOT_CRAN & memes::meme_is_installed()

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  purl = eval_vignette,
  eval = eval_vignette
)

See package website for full vignette

The Bioconductor build system does not have the MEME Suite installed, therefore these vignettes will not contain any R output. To view the full vignette, visit this article page on the memes website at this link

Introduction

memes is an R interface to the MEME Suite family of tools, which provides several utilities for performing motif analysis on DNA, RNA, and protein sequences. It works by detecting a local install of the MEME suite, running the commands, then importing the results directly into R.

Installing the MEME Suite

memes relies on a local install of the MEME Suite. For installation instructions for the MEME suite, see the MEME Suite Installation Guide.

Briefly, the MEME suite can be installed to a default location (~/meme/) on Linux, MacOS, Cygwin, and Windows Linux Subsystem using the following shell commands:

```{bash, eval=F}

As of December 2021, version 5.4.1 is the most recent MEME-Suite version

Please check the install guide (linked above) for more recent information

version=5.4.1 wget http://meme-suite.org/meme-software/$version/meme-$version.tar.gz tar zxf meme-$version.tar.gz cd meme-$version ./configure --prefix=$HOME/meme --with-url=http://meme-suite.org/ --enable-build-libxml2 --enable-build-libxslt make make test make install

For additional troubleshooting or to learn more about install configuration, please see the [Installation Guide](http://meme-suite.org/doc/install.html?man_type=web).

## Detecting the MEME Suite

memes needs to know the location of the `meme/bin/` directory on your local machine.
You can tell memes the location of your MEME suite install in 4 ways. memes
will always prefer the more specific definition if it is a valid path. Here they
are ranked from most- to least-specific:

1. Manually passing the install path to the `meme_path` argument of all memes functions
2. Setting the path using `options(meme_bin = "/path/to/meme/bin/")` inside your R script
3. Setting `MEME_BIN=/path/to/meme/bin/` in your `.Renviron` file, or `export MEME_BIN=/path/to/meme/bin` in your `~/.bashrc`
4. memes will try the default MEME install location `~/meme/bin/`

If memes fails to detect your install at the specified location, it will fall
back to the next option.

To verify memes can detect your MEME install, use `check_meme_install()` which
uses the search herirarchy above to find a valid MEME install. It will report
whether any tools are missing, and print the path to MEME that it sees. This can
be useful for troubleshooting issues with your install.

```r
library(memes)

# Verify that memes detects your meme install
# (returns all green checks if so)
check_meme_install()

# You can manually input a path to meme_path
# If no meme/bin is detected, will return a red X
check_meme_install(meme_path = "bad/path")

FAQS

I get the following error: installation of package 'R.oo' had non-zero exit status

• Problem: Your R installation likely lacks the R.css file
• Solution: when installing the package, set remotes::install_github("snystrom/memes", INSTALL_opts = c("--no-html"))
• NOTE: all help documents for memes will be parsed as plain-text so will lack links or other formatting.

Session Info

sessionInfo()

snystrom/dremeR documentation built on Oct. 13, 2024, 10:48 p.m.