The function returns the inverse of the additive relationship matrix in sparse matrix format for the sex chromosomes (e.g., either X or Z).
makeS(
pedigree,
heterogametic,
DosageComp = c(NULL, "ngdc", "hori", "hedo", "hoha", "hopi"),
returnS = FALSE
)a list:
the model of sex-chromosome dosage compensation assumed.
the sex-chromosome relationship matrix in sparse matrix
form or NULL if returnS = FALSE
the log determinant of the S matrix
the inverse of the S matrix in sparse matrix form
the three column form of the non-zero elements for the inverse of the S matrix
the sex-linked inbreeding coefficients for all individuals in the pedigree
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
A pedigree where the columns are ordered ID, Dam, Sire, Sex
Character indicating the label corresponding to the heterogametic sex used in the “Sex” column of the pedigree
A character indicating which model of dosage compensation.
If NULL then the “ngdc” model is assumed.
Logical statement, indicating if the relationship matrix should be constructed in addition to the inverse
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").
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.
makeS(FG90, heterogametic = "0", returnS = TRUE)
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