makeS {nadiv}

Creates the additive genetic relationship matrix for the shared sex chromosomes

Description

The function returns the inverse of the additive relationship matrix in sparse matrix format for the sex chromosomes (e.g., either X or Z).

Usage

makeS(
  pedigree,
  heterogametic,
  DosageComp = c(NULL, "ngdc", "hori", "hedo", "hoha", "hopi"),
  returnS = FALSE
)

Arguments

pedigree

A pedigree where the columns are ordered ID, Dam, Sire, Sex

heterogametic

Character indicating the label corresponding to the heterogametic sex used in the “Sex” column of the pedigree

DosageComp

A character indicating which model of dosage compensation. If NULL then the “ngdc” model is assumed.

returnS

Logical statement, indicating if the relationship matrix should be constructed in addition to the inverse

Details

Missing parents (e.g., base population) should be denoted by either 'NA', '0', or '*'.

The inverse of the sex-chromosome additive genetic relationship matrix (S-matrix) is constructed implementing the Meuwissen and Luo (1992) algorithm to directly construct inverse additive relationship matrices (borrowing code from Jarrod Hadfield's MCMCglmm function, inverseA) and using equations presented in Fernando & Grossman (1990; see Wolak et al. 2013). Additionally, the S-matrix itself can be constructed (although this takes much longer than computing S-inverse directly).

The choices of dosage compensation models are: no global dosage compensation ("ngdc"), random inactivation in the homogametic sex ("hori"), doubling of the single shared sex chromosome in the heterogametic sex ("hedo"), halving expression of both sex chromosomes in the homogametic sex ("hoha"), or inactivation of the paternal sex chromosome in the homogametic sex ("hopi").

Value

a list:

model

the model of sex-chromosome dosage compensation assumed.

S

the sex-chromosome relationship matrix in sparse matrix form or NULL if returnS = FALSE

logDet

the log determinant of the S matrix

Sinv

the inverse of the S matrix in sparse matrix form

listSinv

the three column form of the non-zero elements for the inverse of the S matrix

inbreeding

the sex-linked inbreeding coefficients for all individuals in the pedigree

vii

a vector of the (non-zero) elements of the diagonal V matrix of the S=TVT' decomposition. Contains the variance of Mendelian sampling for a sex-linked locus

Author(s)

[e-mail]

References

Wolak, M.E., D.A. Roff, and D.J. Fairbairn. in prep. The contribution of sex chromosomal additive genetic (co)variation to the phenotypic resemblance between relatives under alternative models of dosage compensation.

Fernando, R.L. & Grossman, M. 1990. Genetic evaluation with autosomal and X-chromosomal inheritance. Theoretical and Applied Genetics, 80:75-80.

Meuwissen, T.H.E. and Z. Luo. 1992. Computing inbreeding coefficients in large populations. Genetics, Selection, Evolution, 24:305-313.

Examples

 makeS(FG90, heterogametic = "0", returnS = TRUE)