GetCommonQtls: Get common QTLs for phenotypes

In byandell/qtlhot: Inference for QTL Hotspots

Description

Perform joint QTL mapping for phenotypes with marginal LOD peak positions higher than LOD threshold and within set distance of each other

Usage

GetCommonQtls(cross, pheno1, pheno2, thr = 3, peak.dist = 5,
  addcov1 = NULL, addcov2 = NULL, intcov1 = NULL, intcov2 = NULL)

Arguments

cross	object of class cross
pheno1	first phenotype column number or character string name
pheno2	second phenotype column number or character string name; if more than one, then all phenotypes will be tested against pheno1
thr	LOD threshold
peak.dist	maximal peak distance to be considered the same peak (in cM)
addcov1, addcov2	additive covariates for first and second phenotype, respectively
intcov1, intcov2	interactive covariates for first and second phenotype, respectively

References

Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS, Causal model selection hypothesis tests in systems genetics. Genetics (in review).

See Also

CMSTCross

Examples

data(CMSTCross)
commqtls <- GetCommonQtls(CMSTCross, 
                          pheno1 = "y1", 
                          pheno2 = "y3",
                          thr = 3,
                          peak.dist = 5,
                          addcov1 = NULL, 
                          addcov2 = NULL, 
                          intcov1 = NULL, 
                          intcov2 = NULL)
commqtls

byandell/qtlhot documentation built on March 7, 2020, 3:25 p.m.