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altree-add-S - Title...

ALTREE-ADD-S(1p) User Contributed Perl Documentation ALTREE-ADD-S(1p)

NAME

altree-add-S - Title...

SYNOPSIS

altree-add-S [options]
 Options:
    --version             program version
    --short-help|h        brief help message
    --help                help message with options descriptions
    --man                 full documentation
    --first-input-file|i  input file 1
    --second-input-file|j input file 2 data concerning the trait (qualitative or quantitative)
    --output-file|o       output file
    --epsilon|e           epsilon value
    --data-type|t         data type: SNP or DNA
    --proportion|p        proportion of cases in the sample (for qualitative data only)
    --data-qual|q         data type: qualitative or quantitative
    [--outgroup|g]        name of the outgroup
    --low|l               if an haplotype is present equal or less than -l times, the state of S will be set to "?"

OPTIONS

--version
Print the program version and exits.
--short-help
Print a brief help message and exits.
--help
Print a help message with options descriptions and exits.
--man
Prints the manual page and exits.
--first-input-file|i
Input file 1 (paup or phylip file)
--second-input-file|j
Input file 2, contains the number of times a given haplotypes is carried by case and control individuals (qualitative data) or the quantitative values correqsponding to a givent haplotype (quantitative data)
--output-file|o
Output file
--epsilon|e
espilon parameter (see formula in the documentation)
--data-type|t
Type of data: DNA (ATGCU) or SNP (0-1)
--proportion|p
Proportion of case individuals in the sample
--outgroup|g
Name of the outgroup (if it is not in the file containing the number of cases and controls per haplotype)
--data-qual|q
Specify if the data are qualitative or quantitative
--low|l
if an haplotype is present equal or less than -l times, the state of S will be set to "?"

DESCRIPTION

This program adds a new character (called "character S") to each haplotype in the input file according to the number of cases and controls carrying it.
2017-10-06 perl v5.26.0