write.relationshipMatrix: Writing relationshipMatrix in table format

In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description

This function can be used to write an object of class "relationshipMatrix" in the table format used by other software, i.e. WOMBAT or ASReml. The resulting table has three columns, the row, the column and the entry of the (inverse) relationshipMatrix.

Usage

write.relationshipMatrix(
  x,
  file = NULL,
  sorting = c("WOMBAT", "ASReml"),
  type = c("ginv", "inv", "none"),
  digits = 10
)

Arguments

x	Object of class "relationshipMatrix"
file	Path where the output should be written . If NULL the result is returned in R.
sorting	Type of sorting. Use "WOMBAT" for 'row-wise' sorting of the table and "ASReml" for 'column-wise' sorting.
type	A character string indicating which form of relationshipMatrix should be returned. One of "ginv" (Moore-Penrose generalized inverse), "inv" (inverse), or "none" (no inverse).
digits	Numeric. The result is rounded to digits.

Details

Note that "WOMBAT" only uses the generalized inverse relationship matrix and expects a file with the name "ranef.gin", where 'ranef' is the name of the random effect with option 'GIN' in the 'MODEL' part of the parameter file. For ASREML, either the relationship could be saved as "*.grm" or its generalized inverse as "*.giv".

Author(s)

Valentin Wimmer

References

Meyer, K. (2006) WOMBAT - A tool for mixed model analyses in quantitative genetics by REML, J. Zhejinag Uni SCIENCE B 8: 815-821.

Gilmour, A., Cullis B., Welham S., and Thompson R. (2000) ASREML. program user manual. NSW Agriculture, Orange Agricultural Institute, Forest Road, Orange, Australia .

Examples

## Not run: 
# example with 9 individuals
id <- 1:9
par1 <- c(0, 0, 0, 0, 1, 1, 1, 4, 7)
par2 <- c(0, 0, 0, 0, 2, 3, 2, 5, 8)
gener <- c(0, 0, 0, 0, 1, 1, 1, 2, 3)
ped <- create.pedigree(id, par1, par2, gener)
gp <- create.gpData(pedigree = ped)

A <- kin(ped, ret = "add")
write.relationshipMatrix(A, type = "ginv")

## End(Not run)

synbreed documentation built on March 12, 2021, 3:01 a.m.