qtlhot (version 1.2.10)

GetCommonQtls: Get common QTLs for phenotypes

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).

Examples

if (FALSE) {
# Create CMSTCross object
example(SimCrossCausal)
# data(CMSTCross) loaded lazily
commqtls <- GetCommonQtls(CMSTCross, 
                          pheno1 = "y1", 
                          pheno2 = "y3",
                          thr = 3,
                          peak.dist = 5,
                          addcov1 = NULL, 
                          addcov2 = NULL, 
                          intcov1 = NULL, 
                          intcov2 = NULL)
commqtls
}