CMSTtests: Perform CMST Tests on cross object

In byandell/qtlcmst: QTL Causal Model Selection Tests

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, 
  cross.type = c("f2","bc"), method = c("par", "non.par", "joint", "all"),
  penalty = c("bic", "aic", "both"))
CMSTtestsList(cross, pheno1, pheno2, Q.chr, Q.pos,
  addcov1 = NULL, addcov2 = NULL, intcov1 = NULL, intcov2 = NULL, 
  cross.type = c("f2","bc"), method = c("par", "non.par", "joint", "all"),
  penalty = c("bic", "aic", "both"))

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
cross.type	type of cross (bc and f2 for now)
method	test method; see details
penalty	type of penalty; see details

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).

See Also

CMSTCross

Examples

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, 
                  cross.type = "bc",
                  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, 
                  cross.type = "bc",
                  method = "par",
                  penalty = "bic")
out2

byandell/qtlcmst documentation built on May 13, 2019, 9:52 a.m.