I have been using R packages to wrangle genomics data for a few years. Often we have a huge list of parameters including paths to apps, their default parameters, reference genome files and other related files. While it is possible to use R’s default options() function to manage these, often the space becomes quite cluttered.

Recently, I made a using a small package params, which reads configuration files and loads their parameters into R. This attempts to solve a 3 things,

1. easy reading and loading of parameters [load_opts()]
2. dynamic changing of params [set_opts()]
3. fetching and pretty printing of params [get_opts()]

easy loading of params, using tsv files

Basically, load_opts() can automatically recognize a few file extensions, read and load these files:

1. conf/tsv/tab/txt: tab delimited files
2. csv: comma separated
3. xlsx: microsoft excel files (handle with care)

For example, a .conf file is assumed to be tab delimited.

conf = system.file("conf/params.conf", package = "params")
opts = load_opts(conf)

pretty printing

Now if we have a bunch of parameters, it is always easier to see them as a table; get_opts() to the rescue. This uses the nifty kable function from knitr.

get_opts()

|name          |value            |
|:-------------|:----------------|
|default_regex |(.*)             |
|my_conf_path  |~/flowr/conf     |
|my_dir        |path/to/a/folder |
|my_path       |~/flowr          |
|my_tool_exe   |/usr/bin/ls      |
|verbose       |2                |

To extract a specific parameter, simply use get_opts("param_name").

nested parameters

Additionally, there are times where we may have a set of nested parameters; i.e. a former parameter is a part of later. This is quite useful, such that one may define the base path for all the tools (say toolpath), now all other paths would be relative to it:

{{{toolpath}}}/samtools
{{{toolpath}}}/bwa

Taking a simple example, lets use first and last names.

## setting first and last names
## setting full name
set_opts(first = "John", last = "Doe", full_name = '{{{first}}} {{{last}}}')

Now, get_opts("full_name") would reveal John Doe.

automatic checking of file path

Additionally, values of all parameters ending with _exe|_path|_dir are checked by load_opts; whether they exist or not. If they don’t exist a warning (not error) is thrown, informing the user of the issue.

The package is on CRAN, though a more recent development version is available at github.com/sahilseth/params. Also, a detailed readme with examples are available on the sahilseth.com/params.