Runs SuSiE RSS analysis with the specified method. Supports both z+R (correlation matrix) and z+X (genotype matrix) interfaces.
Usage
susie_rss_pipeline(
sumstats,
LD_mat = NULL,
X_mat = NULL,
n = NULL,
L = 30,
L_greedy = 5,
analysis_method = c("susie_rss", "single_effect", "bayesian_conditional_regression"),
coverage = 0.95,
secondary_coverage = c(0.7, 0.5),
signal_cutoff = 0.1,
min_abs_corr = 0.8,
R_finite = NULL,
R_mismatch = NULL,
...
)Arguments
- sumstats
Data frame with 'z' or ('beta' and 'se') columns.
- LD_mat
LD correlation matrix. Mutually exclusive with X_mat.
- X_mat
Genotype matrix (samples x variants). Mutually exclusive with LD_mat.
- n
Sample size.
- L
Maximum number of causal configurations (default: 30).
- L_greedy
Initial greedy number of causal configurations (default: 5).
- analysis_method
One of "susie_rss", "single_effect", "bayesian_conditional_regression".
- coverage
Coverage level (default: 0.95).
- secondary_coverage
Secondary coverage levels (default: c(0.7, 0.5)).
- signal_cutoff
PIP cutoff for selecting top loci (default: 0.1).
- min_abs_corr
Minimum absolute correlation for CS purity (default: 0.8).
- R_finite
Controls variance inflation to account for estimating the R matrix from a finite reference panel. NULL (default): no variance inflation. Passed directly to susie_rss.
- R_mismatch
LD mismatch correction method passed directly to susie_rss. Default NULL disables mismatch correction.
- ...
Additional parameters passed to susie_rss (e.g., var_y).