trans_phased {clipp}

The transmission matrix for phased genotypes

Description

A function to calculate the transmission matrix for a single autosomal genetic locus with an arbitrary number of alleles and phased genotypes, based on Mendel's laws of inheritance. Phased genotypes can be used to investigate parent-of-origin effects, e.g. see (van Vliet et al., 2011).

Usage

trans_phased(n_alleles, annotate = FALSE)

Arguments

n_alleles

A positive integer, interpreted as the number of possible alleles at the genetic locus.

annotate

A logical flag. When FALSE (the default), the function returns a matrix suitable to be used as the trans argument of pedigree_loglikelihood. When TRUE, the function annotates this matrix (and converts it to a data frame) to make the output more easily understood by humans.

Details

When annotate is FALSE, a matrix of genetic transmission probabilities is returned, with rows corresponding to the possible joint parental genotypes and columns corresponding to the possible offspring genotypes. There are ngeno = n_alleles^2 possible phased genotypes, and by choosing an order on these genotypes (which can be viewed by setting annotate to TRUE, see below) we can label the set of possible phased genotypes as 1:ngeno. Then the ⁠(ngeno * gm + gf - ngeno, go)⁠th element of the outputted matrix is the conditional probability that a person has genotype go, given that his or her biological mother and father have genotypes gm and gf, respectively.

When annotate is TRUE, the function converts this matrix to a data frame, adds column names giving the offspring genotype corresponding to each column, and adds columns gm and gf describing the parental genotypes corresponding to each row. In this data frame, phased genotypes are written in the usual form ⁠1|1, 1|2, ...⁠ for the alleles 1:n_alleles, where a|b means the maternal allele is a and the paternal allele is b.

Note that if the output of this function is to be used as the trans argument of pedigree_loglikelihood then the annotate option must be set to FALSE.

Value

Either a matrix of genetic transmission probabilities suitable to be used as the trans argument of pedigree_loglikelihood (if annotate is FALSE), or a data frame that is an annotated version of this matrix (if annotate is TRUE).

References

van Vliet CM, Dowty JG, van Vliet JL, et al. Dependence of colorectal cancer risk on the parent-of-origin of mutations in DNA mismatch repair genes. Hum Mutat. 2011;32(2):207-212.

Examples

# The transition matrix for a biallelic, autosomal locus with phased genotypes
trans_phased(2)
trans_phased(2, annotate = TRUE)