Description Usage Arguments Details Value References Examples
Fit a single-QTL model at a single putative QTL position and get detailed results about estimated coefficients and individuals contributions to the LOD score.
1 2 3 4 |
genoprobs |
A matrix of genotype probabilities, individuals x genotypes |
pheno |
A numeric vector of phenotype values (just one phenotype, not a matrix of them) |
kinship |
Optional kinship matrix. |
addcovar |
An optional matrix of additive covariates. |
nullcovar |
An optional matrix of additional additive covariates that are used under the null hypothesis (of no QTL) but not under the alternative (with a QTL). This is needed for the X chromosome, where we might need sex as a additive covariate under the null hypothesis, but we wouldn't want to include it under the alternative as it would be collinear with the QTL effects. |
intcovar |
An optional matrix of interactive covariates. |
weights |
An optional vector of positive weights for the
individuals. As with the other inputs, it must have |
contrasts |
An optional matrix of genotype contrasts, size
genotypes x genotypes. For an intercross, you might use
|
model |
Indicates whether to use a normal model (least
squares) or binary model (logistic regression) for the phenotype.
If |
se |
If TRUE, calculate the standard errors. |
hsq |
(Optional) residual heritability; used only if
|
reml |
If |
tol |
Tolerance value for linear regression by QR decomposition (in determining whether columns are linearly dependent on others and should be omitted) |
maxit |
Maximum number of iterations in logistic regression
fit (when |
For each of the inputs, the row names are used as individual identifiers, to align individuals.
If kinship
is absent, Haley-Knott regression is performed.
If kinship
is provided, a linear mixed model is used, with a
polygenic effect estimated under the null hypothesis of no (major)
QTL, and then taken as fixed as known in the genome scan.
A list containing
coef
- Vector of estimated coefficients.
SE
- Vector of estimated standard errors (included if se=TRUE
).
lod
- The overall lod score.
ind_lod
- Vector of individual contributions to the LOD score.
Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324.
Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178:1709–1723.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | # load qtl2geno package for data and genoprob calculation
library(qtl2geno)
# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))
# insert pseudomarkers into map
map <- insert_pseudomarkers(iron$gmap, step=1)
# calculate genotype probabilities
probs <- calc_genoprob(iron, map, error_prob=0.002)
# grab phenotypes and covariates; ensure that covariates have names attribute
pheno <- iron$pheno[,1]
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)
# leave-one-chromosome-out kinship matrix for chr 7
kinship7 <- calc_kinship(probs, "loco")[[7]]
# scan chromosome 7 to find peak
out <- scan1(probs[,7], pheno, kinship7, addcovar=covar)
# find peak position
max_pos <- rownames(max(out, map[7]))
# fit QTL model just at that position
out_fit1 <- fit1(probs[[7]][,,max_pos], pheno, addcovar=covar)
# fit QTL model just at that position, with polygenic effect
out_fit1_pg <- fit1(probs[[7]][,,max_pos], pheno, kinship7, addcovar=covar)
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