Usage
nullSim(y,x,gdat,ped,gmap,ids,method=c("permutation","gene dropping"),
vc=NULL,intcovar=NULL,minorGenoFreq=0.05,rmv=TRUE,nit=25,ntimes=10)Arguments
y
a numeric vector or a numeric matrix of one column (representing a phenotype for instance).
x
a data frame or matrix, representing covariates if not missing.
gdat
genotype data without missing values. Should be a matrix or a data frame, with each row representing an observation and each column a marker locus. Ignored in the case of gene dropping.
ped
a pedigree, which is a data frame (id, sex, sire, dam, ...). In "sex", male should be "M", "Male" or 1, and female should be "F", "Female" or 2 (other than 0 and 1). If given, "generation" can be numeric 0, 1, 2, ... or non-numeric "F0", "F1", "F2", ... N
gmap
a genetic map. Should be data frame (snp, chr, dist, ...), where "snp" is the SNP (marker) name, "chr" is the chromosome where the "snp" is, and "dist" is the genetic distance in centi-Morgan (cM) from the leftmost SNP (marker) on the chromosome. Ignored
ids
IDs of the individuals in the data, whose values are given by y in the order. Ignored in the case of permutation.
method
permutation or gene dropping.
vc
an object from estVC or aicVC, or an estimated variance-covariance matrix induced by relatedness. The scan will assume no polygenic variation if vc intcovar
Covariates that interact with QTL.
minorGenoFreq
specify the minimum tolerable minor genotype frequency at a scanning locus if gdat is used.
rmv
a logical variable. If true, then the scanning locus will be skipped if the minor genotype frequency at the locus is smaller than minorGenoFreq. Otherwise, the scanning process will stop and return with NULL.
nit
number of iterations to call optim for optimization. Ignored if vc is NULL. ntimes
number of simulations.