runPhyloBiasCheck: Check for phylogenetic bias

In snaketron/genphen: genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)

Description

Given a set of genotypes such as single nucleotide polymorphisms (SNPs) or single amino acid polymorphisms (SAAPs) for a set of N individuals, the procedure can operate in two modes:

1) it computes a NxN kinship matrix (matrix populated with pairwise distances (Hamming) between each two individuals computed using all the genotypes). Based on the kinship matrix it then estimates the degree of phlyogenetic bias related to each genotype as 1-mean.phylo.dist(allele)/mean.phylo.dist(all)

2) it uses a precomputed kinship matrix and then estimates the degree of phlyogenetic bias related to each genotype using the same procedure.

Usage

runPhyloBiasCheck(input.kinship.matrix, genotype)

Arguments

genotype	Character matrix/data frame or a vector, containing SNPs/SAAPs as columns or alternatively as DNAMultipleAlignment or AAMultipleAlignment Biostrings object.
input.kinship.matrix	precomputed kinship matrix provided by the user.

Details

Input:

• genotype P genotypes of N individuals in the form of NxP character matrix/data frame or vector (if P = 1).

• input.kinship.matrix precomputed NxN matrix (row/column for each individual)

Value

Genotype parameters:

site	id of the site (e.g. position in the provided sequence alignment)
genotype	allele of a SNP or amino acid of SAAP
bias	number between 0 (no bias) or 1 (complete bias)

Mutation bias:

site	id of the site (e.g. position in the provided sequence alignment)
mutation	allele of a SNP or amino acid of SAAP
bias	number between 0 (no bias) or 1 (complete bias) for the mutation computed as max(bias in genotype 1, bias in genotype 2)

Kinship matrix:

kinship.matrix

NxN matrix

Author(s)

Simo Kitanovski <[e-mail]>

See Also

runDiagnostics, runGenphen

Examples

# genotype inputs:
data(genotype.saap)
# phenotype inputs:
data(phenotype.saap)

# phylogenetic bias analysis
bias <- runPhyloBiasCheck(input.kinship.matrix = NULL,
                          genotype = genotype.saap)

snaketron/genphen documentation built on Oct. 1, 2021, 8:09 a.m.