remlf90: R functions for interfacing remlf90 software

In camult/easyGEN: R functions for interfacing BLUPf90 family softwares

R functions for interfacing remlf90 software

Description

The function uses the model formula language in R to describe the model and from this generates the files needed to do an analysis using remlf90 software!

Usage

remlf90(formula, phen, ped = NULL, geno = NULL, map = NULL, idName,
  diffVAR = NULL, nMaternal = NULL, weight = NULL, Inb = FALSE,
  covariate = 0, OPTeff = NULL, OPTlist = NULL, missing = 0,
  Gcov = NULL, Rcov = NULL, execute = TRUE, PED_DEPTH = 0, covAM = 1,
  covR = 1, useF = FALSE)

Arguments

formula	A two-sided linear formula object describing the fixed effects part of the model, with the responses on the left of a ~ operator (separated by "|" if more then one response) and the terms, separated by + operators, on the right.
phen	Name of phenotype file.
ped	Name of pedigree file
geno	Name of genotype file.
map	Name of map file.
idName	Identification name of animal's column.
diffVAR	List of the trait and their unique effect, if any.
nMaternal	Number of traits on maternal effect. By default nMaternal=0.
weight	name of the column (numeric) with a vector of weights, may be NULL. If weights is not NULL, the residual variance of each data-point is set to be proportional to the inverse of the squared-weight.
Inb	Whether to run the inbupgf90 to compute the coefficient of inbreeding. By default Inb=FALSE.
covariate	Name of covariate(s) if there is(are) any.
OPTeff	OPTIONAL effect, i.e., mat, pe, mpe. It is NULL if it is not given.
OPTlist	OPTIONAL effect. It is NULL if it is not given.
missing	a integer specifying the missing value (default 0).
Gcov	Genetic (co)variance. It is NULL if it is not given.
Rcov	Residual (co)variance. It is NULL if it is not given.
execute	Whether to run the remlf90. By default execute=TRUE.
PED_DEPTH	a integer specifying the depth of pedigree search. The default is 3, byt all pedigrees are loaded if it is set to 0.
covAM	type 0 if covariance between additive and maternal genetic effects must be fixed in zero, 1 otherwise. By default covAM=1.
covR	type 0 if covariance between additive and maternal genetic effects must be fixed in zero, 1 otherwise. By default covAM=1.
useF	logical value indicating whether inbreeding coefficient of this animal should be computed. Default is FALSE.

Value

BLUPf90 results.

References

Misztal I, Tsuruta S., Lourenco D., Aguilar I., Legarra A., Vitezica Z (2014). Manual for BLUPF90 family of programs. Available at: <http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=blupf90_all1.pdf>.

camult/easyGEN documentation built on Oct. 22, 2023, 11:59 a.m.