End-to-end pipeline for summary statistics fine-mapping via SuSiE RSS. Supports both z+R (correlation matrix) and z+X (genotype matrix) interfaces.
Usage
rss_analysis_pipeline(
sumstat_path,
column_file_path,
LD_data,
n_sample = 0,
n_case = 0,
n_control = 0,
region = NULL,
skip_region = NULL,
extract_region_name = NULL,
region_name_col = NULL,
qc_method = c("slalom", "dentist", "none"),
finemapping_method = c("susie_rss", "single_effect", "bayesian_conditional_regression"),
finemapping_opts = list(L = 20, L_greedy = 5, coverage = c(0.95, 0.7, 0.5),
signal_cutoff = 0.025, min_abs_corr = 0.8),
impute = TRUE,
impute_opts = list(rcond = 0.01, R2_threshold = 0.6, minimum_ld = 5, lamb = 0.01),
pip_cutoff_to_skip = 0,
R_finite = NULL,
R_mismatch = NULL,
keep_indel = TRUE,
comment_string = "#",
diagnostics = FALSE
)Arguments
- sumstat_path
File path to the summary statistics.
- column_file_path
File path to the column mapping file.
- LD_data
A list from load_LD_matrix containing LD_matrix, LD_variants, ref_panel, block_metadata, and is_genotype flag. When is_genotype=TRUE (from return_genotype=TRUE), LD_matrix contains genotype X and susie_rss uses the z+X interface. Local R is computed only for QC stages that require a correlation matrix.
- n_sample
Sample size. If 0, retrieved from the sumstat file.
- n_case
Number of cases (for case-control studies).
- n_control
Number of controls (for case-control studies).
- region
Region string "chr:start-end" for tabix subsetting.
- skip_region
Character vector of regions to skip (format "chrom:start-end").
- extract_region_name
Gene/phenotype name to subset.
- region_name_col
Column to filter for extract_region_name.
- qc_method
Summary-statistic QC method.
"slalom"and"dentist"run basic allele harmonization plus LD-mismatch QC;"none"runs basic allele harmonization only.- finemapping_method
One of "susie_rss", "single_effect", "bayesian_conditional_regression".
- finemapping_opts
List of fine-mapping options (L, L_greedy, coverage, signal_cutoff, min_abs_corr).
- impute
Whether to impute missing variants via RAISS (default TRUE).
- impute_opts
List of imputation options (rcond, R2_threshold, minimum_ld, lamb).
- pip_cutoff_to_skip
PIP threshold for early stopping (default 0, no skip).
- R_finite
Controls variance inflation to account for finite reference LD. Passed to
susieR::susie_rss().- R_mismatch
LD mismatch correction method passed to
susieR::susie_rss(). Default NULL disables mismatch correction.- keep_indel
Whether to keep indel variants (default TRUE).
- comment_string
Comment character for sumstat file (default "#").
- diagnostics
Whether to include diagnostic info (default FALSE).