CMSTtests: Perform CMST Tests on cross object

Description

Performs 6 separate CMST tests (3 versions, 2 penalties).

Usage

CMSTtests(cross, pheno1, pheno2, Q.chr, Q.pos,
  addcov1 = NULL, addcov2 = NULL, intcov1 = NULL, intcov2 = NULL, 
  method = c("par", "non.par", "joint", "all"),
  penalty = c("bic", "aic", "both"), verbose = FALSE)
CMSTtestsList(cross, pheno1, pheno2, Q.chr, Q.pos,
  addcov1 = NULL, addcov2 = NULL, intcov1 = NULL, intcov2 = NULL, 
  method = c("par", "non.par", "joint", "all"),
  penalty = c("bic", "aic", "both"), verbose = TRUE)

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

Q.chr

QTL chromosome (number or label)

Q.pos

QTL position in cM

addcov1, addcov2

additive covariates for first and second phenotype, respectively

intcov1, intcov2

interactive covariates for first and second phenotype, respectively

method

test method; see details

penalty

type of penalty; see details

verbose

verbose printout if TRUE

Details

Explain method and penalty here.

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

Run this code

# NOT RUN {
data(CMSTCross)
nms <- names(CMSTCross$pheno)
out1 <- CMSTtests(CMSTCross, 
                  pheno1 = nms[1], 
                  pheno2 = nms[2],
                  Q.chr = 1,
                  Q.pos = 55,
                  addcov1 = NULL, 
                  addcov2 = NULL, 
                  intcov1 = NULL, 
                  intcov2 = NULL, 
                  method = "all",
                  penalty = "both")
out1[1:6]
out1[7]
out1[8:12]
out1[13:17]
## list of phenotypes
out2 <- CMSTtests(CMSTCross, 
                  pheno1 = nms[1], 
                  pheno2 = nms[-1],
                  Q.chr = 1,
                  Q.pos = 55,
                  addcov1 = NULL, 
                  addcov2 = NULL, 
                  intcov1 = NULL, 
                  intcov2 = NULL, 
                  method = "par",
                  penalty = "bic")
out2
# }

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