Removes markers that are uninformative or poorly genotyped: those below a minor allele frequency threshold, those called in too few individuals, and optionally those that are monomorphic.
Usage
filterMarkers(x, ...)
# S4 method for class 'BreedingExperiment'
filterMarkers(
x,
min_maf = 0.01,
min_call_rate = 0.9,
drop_monomorphic = TRUE,
...
)Arguments
- x
A BreedingExperiment object.
- ...
Unused.
- min_maf
Minimum minor allele frequency to keep.
- min_call_rate
Minimum proportion of individuals with a call.
- drop_monomorphic
Drop markers with no variation.
Value
A BreedingExperiment object with fewer rows.
Examples
set.seed(1)
be <- simulateBreeding(n_ind = 30, n_marker = 100, missing = 0.05)
nrow(be)
#> [1] 100
nrow(filterMarkers(be, min_maf = 0.05, min_call_rate = 0.9))
#> [1] 90