ibdhap.reduce.states: ibdhap reduce states

In IBDhaploRtools: Functions for the Analysis of IBD Haplo Output.

Description

This function reduces the columns of a qibd.out file created by ibd_haplo by summing probabilities over certain columns. When reducing an output file that was run on haplotypes, this script will sum over columns 1-8 (other), 9-10 (2 pairs chrs. ibd), 11-14 (one pair of chrs. ibd),and 15 (no ibd). When reducing a file from genotypic date, the corresponding columns are summed over so that they reflect the same values ( other, one pair ibd, two pairs ibd, not ibd). A file will then be output with these probabilites displayed just like the original ibd_haplo output qibd file.

Usage

ibdhap.reduce.states(qibd.filename, dat.filename, output.filename)

Arguments

qibd.filename	The filename of the qibd.out file the is produced from running ibd_haplo. This is to be input as a character string. In the examples, this file is called "qibd_g.gold".
dat.filename	The filename of the .dat file used to run ibd_haplo. This is the complicated parameter file that consists of three lines of values / indicators that tells ibd_haplo what to do. In the examples, this files is called "compu_4haps.dat".
output.filename	The name of the file that this function will print to. In the examples, this filename is "test.file.txt".

Value

A txt document the looks exactly like the qibd file input, but the ibd state probabilities per marker are summed over in the manner described above.

Author(s)

MD Brown

Examples

## See vignette("IBDhaploRtools_tutorial" )

IBDhaploRtools documentation built on May 2, 2019, 6:48 p.m.