getIBDposterior: IBD Posterior Probabilities

In bahlolab/isoRelate: Identity-by-Descent Inference of Haploid Recombining Organisms

Description

getIBDposterior() calculates the posterior probabilities of IBD sharing between pairs of isolates.

Usage

getIBDposterior(ped.genotypes, parameters, number.cores = 1, error = 0.001)

Arguments

ped.genotypes	A list containing 2 objects. See the Value description in getGenotypes for more details on this input.
parameters	A data frame containing meioses and IBD probability estimates for all pairwise combinations of isolates. See the Value description in getIBDparameters for more details on this input.
number.cores	Positive integer. The number of cores used for parallel execution.
error	The genotyping error rate. The default value is 0.001.

Value

A data frame with the first four columns:

1. Chromosome

2. SNP identifiers

3. Genetic map distance

4. Base-pair position

where each row describes a single SNP. These columns are headed chr, snp_id, pos_M and pos_bp respectively. Columns 5 onwards contain the posterior probabilities for each pair of isolates, where a single column corresponds to one pair of isolates. These columns are labeled with merged family IDs and isolate IDs separated by a slash symbol (/).

Examples

## Not run: 
# calculate the posterior probability of IBD sharing
# note: this can take a while to run if there are many pairs
my_posterior <- getIBDposterior(ped.genotypes = png_genotypes,
                                parameters = png_parameters,
                                number.cores = 1,
                                error = 0.001)

head(my_posterior[,1:10])

## End(Not run)

bahlolab/isoRelate documentation built on May 11, 2019, 5:25 p.m.