Loads genotype data for a region via loadLdMatrix(returnGenotype=TRUE)
and removes monomorphic variants. Returns the raw genotype matrix and
metadata, which callers can use to derive either a correlation matrix R (for
summary-based weight training or fine-mapping) or an SVD (for TWAS z-score
computation).
Arguments
- ldMetaFilePath
Path to the LD metadata TSV file.
- region
Region of interest: "chr:start-end" string or data.frame with chrom/start/end.
- nSample
Optional original panel sample size for computing variance (= 2*p*(1-p)*n/(n-1)). Passed through to
loadLdMatrix().
Value
An LdData S4 object with monomorphic variants removed.
Consumers should use S4 accessors: getGenotypes(),
getRefPanel(), getVariantIds(). The number of sketch samples
is nrow(getGenotypes(result)).
Examples
meta <- system.file("extdata", "ld_reference", "ld_meta_file.tsv",
package = "pecotmr")
loadLdSketch(ldMetaFilePath = meta, region = "chr22:16000000-18000000")
#> LdData: 130 variants
#> Correlation: NULL, Genotype handle: available
#> Reference N: 1000