Extract a genotype matrix for a subset of SNPs from a
GenotypeHandle. Returns a RangedSummarizedExperiment
with dosage assay in Bioconductor convention (variants x samples),
variant metadata as rowRanges (GRanges), and sample IDs as
colData.
Usage
extractBlockGenotypes(handle, snpIdx, meanImpute = TRUE)
Arguments
- handle
A GenotypeHandle object.
- snpIdx
Integer vector of 1-based SNP indices into
handle@snpInfo.
- meanImpute
Logical, whether to mean-impute missing values.
Default TRUE.
Value
A RangedSummarizedExperiment with:
- assay("dosage")
Numeric matrix (variants x samples)
- rowRanges
GRanges with A1, A2 metadata
- colData
DataFrame with sampleId column