README.md

In gact/shmootl: QTL Analysis Utilities for Yeast

ShmooTL: QTL analysis utilities for yeast

This package contains pipelines and utilities for QTL analysis of yeast cross data. Pipelines can be run from the command line or from within the R environment. Utility functions are available from within R.

To find more information on using ShmooTL, see the Usage and Documentation sections.

Dependencies

This package depends on the following:

• argparser
• Bioconductor
• Biostrings
• funqtl
• qtl
• qtlcharts
• rhdf5
• rtracklayer
• VariantAnnotation
• yaml

In addition, the following suggested packages are each needed for a specific use:

• abind: estimating FDR in single-QTL analysis
• viridis: plotting with the Viridis palette
• xlsx: writing Excel output

Installation

Before installing ShmooTL from GitHub, you will first need to install its dependency packages.

Installing packages from R

Some required packages can be installed from within R as follows:

install.packages('argparser')
install.packages('qtl')
install.packages('yaml')

Suggested packages abind, viridis and xlsx can also be installed in this way:

install.packages('abind')
install.packages('viridis')
install.packages('xlsx')

Installing Bioconductor packages

To install required Bioconductor packages (e.g. VariantAnnotation, rhdf5), see the Bioconductor installation documentation page.

Installing packages from GitHub

Packages funqtl and qtlcharts can be installed directly from the GitHub website, but you must first install the devtools package, which can be installed from within R:

install.packages('devtools')

To install funqtl from GitHub, input:

library(devtools)
install_github('ikwak2/funqtl')

To install qtlcharts from GitHub, install the package hmtlwidgets as follows:

install.packages('htmlwidgets')

Then install qtlcharts from GitHub:

library(devtools)
install_github('kbroman/qtlcharts')

Installing ShmooTL from GitHub

With the devtools package and other dependencies installed, ShmooTL can be installed from GitHub as follows:

library(devtools)
install_github('gact/shmootl')

If you want to access vignettes for the installed package, set the build_vignettes option to TRUE, as follows:

library(devtools)
install_github('gact/shmootl', build_vignettes=TRUE)

ShmooTL vignettes can then be accessed as described in the Documentation section.

Usage

Package pipelines can be run from the command line using Rscript as follows:

Rscript -e 'library(shmootl)' -e 'run()' <pipeline> [-h] [<args>]

...where run is the general ShmooTL pipeline-running function, <pipeline> is the name of the pipeline to run, and <args> represents any arguments to be passed to the given pipeline. To see the available options for a pipeline, input the help flag (-h) after the name of the pipeline.

Documentation

To view the ShmooTL help pages within R, input the following command:

help(package=shmootl)

To view the help page for a specific ShmooTL function, input a command such as the following:

help(readCrossCSV)

...where the first argument (in this case readCrossCSV) is the name of the function for which help is being sought.

If package vignettes were built when installing ShmooTL, the ShmooTL user guide can be viewed with the following R command:

vignette('shmootl-guide')

Passing the string 'shmootl-devnotes' to the same function displays the ShmooTL developer notes.

Contact

For further information, contact the package maintainer listed in the package DESCRIPTION file. Please submit any issue on the ShmooTL GitHub repository.

gact/shmootl documentation built on Nov. 11, 2021, 6:23 p.m.