shmootl-package: QTL Analysis Utilities for Yeast
In gact/shmootl: QTL Analysis Utilities for Yeast

Description Item IDs Syntactic Names Package Pipelines See Also References Examples

The shmootl package contains pipelines and functions for QTL analysis in yeast. This package follows many of the conventions on R/qtl, and depends on that package for standard QTL analysis. It also depends on R/funqtl for QTL analysis with time-series phenotypes. See below for links to these packages, as well as key references.

Various items in shmootl (e.g. chromosomes/sequences, markers, samples, phenotypes) have an associated identifier (ID). A valid item ID in shmootl is a string of nonzero length, containing any combination of printable ASCII characters (including letters and numbers), except for a single quote, double quotes, backtick, comma, forward slash, or backslash.

A syntactically valid R name contains only letters, numbers, dots, and underscores. The name should start with a letter, or a dot that is not followed by a number. In addition, specific reserved words are not permitted. Many R packages and functions automatically render item names syntactically valid, so for example, a phenotype name may be changed when added to an R/qtl cross object. For more information, see the relevant R documentation. See also the base R function make.names.

Within shmootl, package pipelines are fully-documented functions that follow specific conventions regarding function name and formal arguments. Pipeline function names are of the form 'run_<pipeline>' (where '<pipeline>' is replaced by the pipeline name).

Package pipelines can be run from a command line with 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. To list all available pipelines, input the help flag (-h) without a pipeline name. (See usage examples below.)

Arends D, Prins P, Jansen RC, Broman KW (2010) R/qtl: high-throughput multiple QTL mapping. Bioinformatics 26(26):2990-2. (PubMed)

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890. (PubMed)

Kwak IY, Moore CR, Spalding EP, Broman KW (2014) A simple regression-based method to map quantitative trait loci underlying function-valued phenotypes. Genetics 197(4):1409-16. (PubMed)

## Not run: 
# To list available pipelines from the command line.
Rscript -e 'library(shmootl)' -e 'run()' -h

# To run the 'scanone' pipeline from the command line.
Rscript -e 'library(shmootl)' -e 'run()' scanone \
    --infile input.csv --h5file output.hdf5

# To run the 'scanone' pipeline from within R.
run_scanone(infile='input.csv', h5file='output.hdf5')

## End(Not run)