Usage
scanone.perm(pheno, pheno.col = 1, probs, addcovar, intcovar, snps, model = c("additive", "full"), path = ".", nperm = 1000)
Arguments
pheno
data.frame containing phenotype data. Required. rownames must contain sample IDs and there must be a column labelled 'sex' to perform correct mapping on the X chromosome.
pheno.col
numeric or character vector: Either a vector of number that indicate columns to use or a set of column names in pheno.
probs
3D numeric array, containing the founder haplotype contributions or genotype probabilities. The sample IDs, founder letter codes and markers IDs must be in dimnames.
addcovar
data.frame or numeric matrix, containing any additive covariates. Sample IDs must be in rownames.
intcovar
data.frame or numeric matrix, containing any covariates that interact with the QTL. Sample IDs must be in rownames.
snps
data.frame containing 4 columns with marker location information. SNP ID, chr, Mb, cM in columns 1 through 4, respectively.
model
Character string, containing one of "additive" or "full", indicating the type of model to fit.
path
Character string containing the location where permutation results should be written.
nperm
Numeric, containing the number of permutations to run.