Filter monomorphic markers. This filter will remove from the dataset markers with just one genotype phenotype:
genotypes are ALL homozygotes REF/REF (pp)
genotypes are ALL heterozygotes REF/ALT, ALT/REF (pq or qp)
genotypes are ALL homozygotes ALT/ALT (qq)
Filter targets: SNPs
Statistics: the number of genotype phenotypes
Used internally in radiator and might be of interest for users who wants to keep only polymorphic markers in their dataset.
filter_monomorphic(
data,
filter.monomorphic = TRUE,
parallel.core = parallel::detectCores() - 1,
verbose = FALSE,
...
)
(4 options) A file or object generated by radiator:
tidy data
Genomic Data Structure (GDS)
How to get GDS and tidy data ?
Look into tidy_genomic_data
,
read_vcf
or
tidy_vcf
.
(optional, logical)
Default: filter.monomorphic = TRUE
.
(optional) The number of core used for parallel
execution during import.
Default: parallel.core = parallel::detectCores() - 1
.
(optional, logical) When verbose = TRUE
the function is a little more chatty during execution.
Default: verbose = TRUE
.
(optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)
A list with the filtered input, whitelist and blacklist of markers..