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README

The "tdthap" package
====================

This file contains "tdthap" as an R package. This package implements much of 
the work described in: 

Clayton, D. and Jones, H.B. (1999), Transmission/disequilibrium tests for 
extended marker haplotypes, Am.J.Hum.Gen., 65:1161-1169.

Note that, in common with that paper, no satisfactory solution is offered 
in this distribution for the problem of phase uncertainty for haplotype 
assignment --- omission of phase-uncertain data is the only remedy (and this
has its pitfalls).

You should be aware that this is very experimental software at present and 
it comes with absolutely no guarantees.

If you don't have R yet, you should have! R is available from CRAN (the 
Comprehensive R Archive Network) at 

http://www.ci.tuwien.ac.at/R/contents.html

and various mirror sights world-wide. If you are new to R, I recommend that 
you also download the faq document! R is a dialect of the S language for 
statistics and graphics, and I shall shortly add an Splus version to 
this distribution. 

After unzipping and untarring the distribution you will have this file, a 
short test "pedfile", and a sub-directory called tdthap/. If you are 
installing the package in the main system R library, all you have to do is, 
from the current directory,

R CMD INSTALL tdthap

If the install is OK you should now be able to go into R and use the package.
At the R prompt this is done by

library(tdthap)

Once the library is successfully loaded you should
follow the instructions in the documentation. For R novices, to read 
LINKAGE "pedfiles", you can use read.table(). If the file contains a 
header line which defines the variable names, 

ped <- read.table("myfile.ped", header=T)

should work (although you may also need to define the field separator eg. 
sep="\t" for a tab delimited file). If the header line is not present, use

ped <- read.table("myfile.ped", rownames=NULL)

read.table() uses lots of memory and you might need more than the default. 
To start R with more memory use the -v and -n options on the command line 
(see the "man" page)


To load the package in the system-wide R library you may need system 
permissions. If you want to load the package in a private library, eg.
/home/me/R/library, then you should install with 

R CMD INSTALL tdthap -l /home/me/R/library

You should remember then that R needs to know about this directory. This can 
be done by appending this to the variable .lib.loc (perhaps in your 
.First function or your .Rprofile file), as follows

.lib.loc <- c("/home/me/R/library", .lib.loc)

Alternatively, the R_LIBS environment variable can be used to specify search 
paths for private libraries.

After installation of the library,  the html help files can be accessed via 
the online help system, which can be strated up using the help.start() command.
They are stored in  

(library directory)/tdthap/html  

LaTex versions are also available in 

(library directory)/tdthap/latex

The library includes C code and, therefore, a C compiler is required. R
is available for Windows, but I have no experience of installing R libraries
in Windows. I can only say that this works on Sun (Solaris) and Linux 
platforms.




In order to test installation, I have included a small test pedigree file. 
To read this into R as a  dataframe, you need to type

testped <- read.table("test.ped")

The functions require the dataframe to be in this standard LINKAGE format.


David Clayton

Diabetes and Inflammation Laboratory		Tel: 44 (0)1223 762669 
Cambridge Institute for Medical Research	Fax: 44 (0)1223 762102
Wellcome Trust/MRC Building			david.clayton@cimr.cam.ac.uk
Addenbrooke's Hospital, Cambridge, CB2 2XY	www-gene.cimr.cam.ac.uk/todd/


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