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.