CMSTtests: Perform CMST Tests on cross object

Description Usage Arguments Details References See Also Examples

Description

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

Usage

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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

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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.