runPhyloBiasCheck: Check for phylogenetic bias

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/genphen.R

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

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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:

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 <simo.kitanovski@uni-due.de>

See Also

runDiagnostics, runGenphen

Examples

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# 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 Aug. 2, 2019, 2:07 p.m.