GAS Manual

--{- Footnotes v2.3 -}--

(c) Alan Young, 1993-1998.

This document contains footnotes for the general and analysis manuals for the gas program.

Why use an input file?

This method was chosen to ensure that gas will perform identically on a variety of computer systems. Note that a few results may differ slightly between systems due to different numeric `rounding' conventions used by their output routines.

L-format Description

For a description of l-format see a manual for the LINKAGE programs. The g-format is a superset of l-format, extended to allow sensible naming of things (eg. loci, individuals) and to enable description of a wider range of genetic features (eg. partially-known gentotypes, imprinting).

What is `makeped' ?

`makeped' is part of the LINKAGE suite of programs and serves to pre-process data for other individual programs. gas incorporates features analagous to those provided by makeped transparently during the input stage.

The Normal Distribution

The `normal' distribution is also known as the `Gaussian Distribution' or `Error Function' in some statistical and mathematical texts.

Use of Alsize Format

The alsize (allele size) format is generally used for reading CA-repeat marker data from automated fluorescent genotyping machines, however it can also be used for any other form of data where the identity of an allele can be directly inferred from the size of a floating point variable.

Examples of good names for loci ?

The names 314, fred, big_bad_alice and John6 are all allowable, but 2b is not.

Apparent Illegitimacy

A common cause of apparent illegitimacy is a heterozygous subject being marked as homozygous by the genotyping program before the data reached gas.

How files were archived under Unix

The files making up the gas distribution set were archived with the command:

tar -cvf - * | compress > bundlefile

Extra Parameters

The internal gas help system may list more parameters for a routine than are described in the manual. These are either present for debugging purposes or are present as a result of specific tasks programmed on a contract basis. Such undocumented parameters should not be used except by arrangment with the author of gas.

What is a Discordant Pair

A discordant pair (usually referring to siblings) is one in which one memmber is affected and the other is not.