cnF2freq: Calculating Inheritance Probabilities using cnF2freq
In MCIBD: Monte Carlo Identity-By-Descent Matrix Estimation

Description Usage Arguments Details Value Author(s) References See Also Examples

cnF2freq is used to run the cnF2freq program or even compile cnF2freq in different operating systems. Usually on a shared cluster, compiling is required for the first time usage.

1	cnF2freq(ped.file, chr.file, os = "unix", compile = FALSE)

`ped.file`	a file containing pedigree information. (See `pedi.ric` in `other.zip` or `other.tar` for example.)
`chr.file`	a file containing chromosome marker information. (See `chro.ric` in `other.zip` or `other.tar` for example.)
`os`	a string specifying the operating system, typically "unix" or "linux" or "windows".
`compile`	logical. If `TRUE`, `cnF2freq` is compiled before running.

For computers with the user authorities, cnF2freq may not need to be compiled.

An output file cnF2freq.out is produced in the working directory.

Xia Shen

Nettelblad, C., Holmgren, S., Crooks, L. and Carlborg, O. (2009). cnF2freq: Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models. Lecture Notes in Bioinformatics (LNBI), 5462: 307-319, Springer-Verlag Berlin Heidelberg.

MCIBD-package

## Unzip other.zip or other.tar in the package library folder. 
## Make sure you are using an operating system with g++ compiler installed.
## Copy the file cnF2freq.cpp in the working directory.
## Execute this function, setting compile = TRUE.

## You may also copy the file cnF2freq_unix or cnF2freq_linux 
## or cnF2freq_windows.exe, then with user authority, 
## this function can be executed without compiling.