Run reusable individual-level QC
Usage
qc_individual_data(
X,
Y,
maf = NULL,
X_variance = NULL,
missing_rate_thresh = NULL,
maf_cutoff = 5e-04,
xvar_cutoff = 0,
ld_reference_meta_file = NULL,
keep_indel = TRUE,
pip_cutoff_to_skip = 0,
context = NULL
)Arguments
- X
Genotype matrix or named list of genotype matrices.
- Y
Phenotype vector/matrix or named list of phenotype matrices.
- maf
Optional MAF vector or named list.
- X_variance
Optional variant variance vector or named list.
- missing_rate_thresh
Maximum missing genotype rate.
- maf_cutoff
Minimum MAF cutoff.
- xvar_cutoff
Minimum genotype variance cutoff.
- ld_reference_meta_file
Optional LD reference metadata file.
- keep_indel
Whether indel variants are kept during LD-reference filtering.
- pip_cutoff_to_skip
Optional single-effect PIP cutoff.