Usage
assoc.map(pheno, pheno.col = 1, probs, K, addcovar, snps, chr, start, end, model = c("additive", "dominance", "full"), scan = c("one", "two"), output = c("lod", "p-value", "bic"), snp.file = "ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz") assoc.map.perms(pheno, pheno.col = 1, probs, addcovar, snps, model = c("additive", "dominance", "full"), scan = c("one", "two"), output = c("lod", "p-value", "bic"), snp.file = "ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz", nperm = 1000)
Arguments
pheno
Data.frame containing the phenotype data. Sample IDs must be in rownames. One of the columns should be called sex and contain M or FALSE to indicate the sex of each sample.
pheno.col
Either a numeric vector containing column IDs to map in pheno or a vector of column names in pheno.
probs
A 3 dimensional array of genotype probabilities as provided from condense.model.probs
Samples, founder and markers in dims 1:3. All dimensions must have dimnames.
K
Numeric matrix containing kinship values for the samples in pheno and probs. Sample IDs must be in rownames and colnames.
addcovar
Numeric matrix of additive covariates to use in mapping. Sample IDs must be in rownames.
snps
Data.frame containing marker IDs, chromosomes, Mb and cM locations in columns 1:4.
chr
Character containing the chromosome on which to map.
start
Numeric value containing the proximal position for mapping. May be in Mb or base pairs (see Details).
end
Numeric value containing the distal position for mapping. May be in Mb or base pairs (see Details).
model
Character string that is one of "additive", "dominance" or "full". Indicates the type of model to fit. Note that the probs must match the type of model being fit. See condense.model.probs
to output different probs.
scan
Character string that is either "one", or "two" indicating whether a single scan or a pairwise scan should be performed across the interval.
output
Character string that is either "lod", "p-value" or "bic" indicating the mapping statistic to return.
nperm
Integer indicating the number of permutations to perform. Default = 1000.