CMSTtests {qtlcmst} | R Documentation |
Performs 6 separate CMST tests (3 versions, 2 penalties).
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"))
cross |
object of class |
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 |
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 ( |
method |
test method; see details |
penalty |
type of penalty; see details |
Explain method and penalty here.
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).
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