GetCommonQtls function

Get common QTLs for phenotypes

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

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