Interval mapping (qtl::scanone()) or composite interval mapping
(qtl::cim()) for one trait, with a genome-wide LOD threshold from
permutations (Churchill and Doerge 1994). For each linkage group whose
highest LOD passes the threshold, the peak is reported with its
1.5-LOD support interval, nearest marker, genome-wide p-value, percentage
of phenotypic variance explained and estimated effects.
Usage
scan_qtl(
cross,
trait = NULL,
method = "hk",
cim = FALSE,
n_marcovar = 3,
window = 10,
n_perm = 1000,
alpha = 0.05,
step = 1,
seed = 1,
progress = NULL
)Arguments
- cross
A cross from
build_cross().- trait
Trait name.
- method
One of
qtl_methods().- cim
Use composite interval mapping.
- n_marcovar, window
Marker covariates and window (cM) for CIM.
- n_perm
Number of permutations.
- alpha
Genome-wide significance level.
- step
Spacing (cM) of the scan.
- seed
Random seed.
- progress
Optional function called with the share done (0 to 1).