getLocusMatrix: XIBD Binary IBD Matrix

In bahlolab/XIBD: Identity-by-Descent Analysis of the Human Genome

Description

Returns a binary matrix of IBD (1) and non-IBD (0) for each SNP and pair combination.

Usage

getLocusMatrix(ped.genotypes, ibd.segments)

Arguments

ped.genotypes	a named list containing pedigree, genotypes and model. See Value description in getGenotypes for more details. The family IDs and individual IDs in pedigree must match the family IDs and individual IDs in the header of genotypes.
ibd.segments	a named list containing the ibd_segments inferred from pairs of samples. See value description in getIBDsegments for more details.

Value

A data frame the first four columns:

1. Chromosome (type "character", "numeric" or "integer")

2. SNP identifiers (type "character")

3. Genetic map distance (centi morgans, cM) (type "numeric")

4. Base-pair position (type "integer")

where each row describes a unique SNP. These columns are headed chr, snp_id, pos_M and pos_bp respectively. Columns 5 onwards contain the binary IBD information for each sample pair, where a single column corresponds to a single pair. These columns are labeled with merged family IDs and individual IDs separated by a slash symbol (/). For example famA/ind1/famA/ind2.

Examples

# generate a binary IBD matrix
my_locus_matrix <- getLocusMatrix(ped.genotypes = example_genotypes,
                                  ibd.segments = example_ibd)

bahlolab/XIBD documentation built on May 11, 2019, 5:24 p.m.