File: README.haplo.stats

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#$Author: sinnwell $
#$Date: 2008/10/03 15:10:39 $
#$Header: /people/biostat3/sinnwell/Haplo/Make/RCS/README.haplo.stats,v 1.13 2008/10/03 15:10:39 sinnwell Exp $
#$Locker:  $
#$Log: README.haplo.stats,v $
#Revision 1.13  2008/10/03 15:10:39  sinnwell
#for version 1.4.0
#
#Revision 1.12  2007/05/09 16:08:46  sinnwell
#for version 1.3.0
#


===================================================================

Brief Description:

Haplo Stats is a suite of S-PLUS/R routines for the analysis of 
indirectly measured haplotypes. The statistical methods assume 
that all subjects are unrelated and that haplotypes are ambiguous 
(due to unknown linkage phase of the genetic markers).

A further description can be found in README within the S-PLUS
package, or the contents of README may be viewed in S-PLUS 
entering the command:

	 library(lib.loc="/INSTALLATION DIR PATH/", help=haplo.stats)

The same information is available in the R package within the files
named INDEX.haplo.stats and DESCRIPTION.haplo.stats.


The main functions in Haplo Stats are:

haplo.em
     for the estimation of haplotype frequencies, and posterior 
     probabilities of haplotype pairs for a subject, conditional 
     on the observed marker data

haplo.glm
     glm regression models for the regression of a trait on 
     haplotypes, possibly including covariates and interactions

haplo.score
     score statistics to test associations between haplotypes 
     and a wide variety of traits, including binary, ordinal,
     quantitative, and Poisson.

seqhap
     sequential haplotype scan methods to perform association analyses
     for case-control data.  When evaluating each locus, loci that 
     contribute additional information to haplotype associations with 
     disease status will be added sequentially.

=================================================================

Installation procedures for haplo.stats

We develop the haplo.stats package in S-PLUS, and we have
translated haplo.stats to be a package in R. Intallation procedures
in this file are for setting up a 'local library' for a user. If a
large group of users plan to use the same library, then install on a
system-wide 'library' location designated by a system administrator.

--------------------------------------------------------------

S-PLUS Installation (unix-like systems)

The haplo.stats S-PLUS functions are written for S-PLUS versions 7.0.6
and 8.0.1.

To install the software for local use in S-PLUS versions prior to
8.0.1, move haplo.stats_x.y.z_S.tar.gz to your chosen installation 
directory and follow the series of commands:

1) gunzip haplo.stats_x.y.z_S.tar.gz
2) tar -xvf haplo.stats_x.y.z_S.tar
3) cd haplo.stats
4) cd src
5) Splus CHAPTER
6) Splus make
7) mv .Data ..
8) mv S.so ..

Installation instructions for S-PLUS 8 are more like the R installation
See www.csan.insightful.com for more details

--------------------------------------------------------------

R Installation (unix-like systems)

For local installation, execute the following command with the local
"INSTALL LIBRARY DIR PATH" correctly specified.  

R CMD INSTALL -l /INSTALL LIBRARY DIR PATH/ haplo.stats_x.y.z_R.tar.gz

Installation instructions for different use may be found on the R project 
website (http://www.r-project.org).


======================================================================

User Documenation:

A manual (manualHaploStats.pdf) is provided in the haplo.stats/doc
directory. Information on the supplied functions can be found within
both the S-PLUS and R systems by typing help(function), where
"function" is the name of the procedure of interest (no quotes
needed). The S-PLUS/R commands used within the user manual are
supplied as a script within the haplo.stats/demo directory. This file
can be used to test the various functions to check the computed output
against the user manual.