Extends standard LDSC to multiple annotation categories, estimating per-annotation contributions to genetic covariance and heritability.
Usage
s_ldsc(
traits,
sample.prev = NULL,
population.prev = NULL,
ld,
wld,
frq,
trait.names = NULL,
n.blocks = 200,
ldsc.log = NULL,
exclude_cont = TRUE
)Arguments
- traits
Character vector of paths to .sumstats.gz files
- sample.prev
Numeric vector of sample prevalences (NULL for continuous traits)
- population.prev
Numeric vector of population prevalences (NULL for continuous)
- ld
Path to annotation LD score directory
- wld
Path to weight LD score directory
- frq
Path to frequency file directory
- trait.names
Character vector of trait names (defaults to V1, V2, ...)
- n.blocks
Number of jackknife blocks (default 200)
- ldsc.log
Log file path (ignored in gsemr)
- exclude_cont
Exclude continuous annotations (default TRUE)
Examples
if (FALSE) { # \dontrun{
# Stratified LDSC requires annotation-specific LD, weight, and freq files.
result <- s_ldsc(
traits = c("T1.sumstats.gz", "T2.sumstats.gz"),
ld = "baseline_LD/",
wld = "weights/",
frq = "frq/",
trait.names = c("V1", "V2")
)
# Feed into `enrich()` for annotation enrichment tests.
} # }