getIBDmatrix: Binary IBD Matrix

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

Description

getIBDmatrix() produces a binary matrix of IBD (1) and non-IBD (0) results for each SNP and isolate pair combination. Each row identifies a unique SNP while each column identifies a unique isolate pair.

Usage

getIBDmatrix(ped.genotypes, ibd.segments)

Arguments

ped.genotypes	A list containing 2 objects. See the Value description in getGenotypes for more details on this input.
ibd.segments	A data frame containing the IBD segments detected by isoRelate. See the Value description in getIBDsegments for more details on this input.

Value

A data frame with 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. Columns 1-4 are headed chr, snp_id, pos_M and pos_bp respectively. Columns 5 onwards contain the binary IBD information for each isolate pair, where a single column corresponds to a single pair. These columns are labeled with merged family IDs and isolate IDs separated by a slash symbol (/). For example fid1/iid1/fid2/iid2.

See Also

getGenotypes, getIBDsegments, getIBDproportion, getIBDiR.

Examples

# generate a binary IBD matrix
my_matrix <- getIBDmatrix(ped.genotypes = png_genotypes,
                          ibd.segments = png_ibd)

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