IBDhaploRtools (version 1.8)

ibdhap.transitions: create transition matrix

Description

Creates a matrix of transition counts from when ibd state switches along the chromosome.

Usage

ibdhap.transitions(calls, data.type = c("h", "g", "r"))

Arguments

calls

The data.frame created from running ibdhap.make.calls on ibd_haplo output.

data.type

"h" : haplotypic data "g" : genotypic data (or hap data ran as genotypic) "r" : reduced data (output from running ibdhap.reduce.states and then ibdhap.make.states)

Value

A matrix of size 15 x 15 (haplotypic) or 9 x 9 (genotypic) that shows counts of ibd state transitions. Element [i,j] of the output is the number of times state i changed to state j in the data.

Details

To create this matrix, all no calls are ignored. This is because, when transitioning out of being relatively certain of an ibd state, the marginal probabilities of ibd state by marker usually move into a segment of uncertainty (hence no calls) before it becomes relatively certain of an ibd state and therefore switches states.

Examples

## this example is taken from the package vignette.
##See vignette(IBDhaploRtools_tutorial)

data(qibd_phased)
data(ids_phased)
data(trueibd_phased)

phased.gold <- ibdhap.make.calls( qibd.file  = qibd_phased,
                   ids.file= ids_phased, cutoff = 0.8)
transitions.phased <- ibdhap.transitions(phased.gold, data.type="h")