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 nb cases/controls per haplotypes
--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
--ancestor|a name of ancestral haplotype
[--outgroup|g] name of the outgroup
[--low|l] disease statut for haplotype carried by one individual
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 - --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) - --low|l If this option is present, it forces the state of the character
- S to be "?" for haplotypes carried by only one individual
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.