Description Usage Arguments Value
This reads options from the command-line, if provided. Also it can replace references to system variables in option values, such as '*' or \$WORK, with fully qualified values. Also translates coordinates which use Gb, Mb, Kb to integer values. All defined options of the form mPhen.xxx are examined and modified.
mPhen.defineOptions(file = NULL, getOptionsFromCommandLine = TRUE)
specified if the options are in a script file and not set manually
If running from a script using command Rscript, then this will read in command line options, such as \'–mPhen.logp=FALSE\'
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