Skip to content

Drop defunct susie_rss flags; add --rss-control to rss_analysis #1396

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
gaow merged 2 commits into from
Jul 30, 2026
+21 −94
Merged

Drop defunct susie_rss flags; add --rss-control to rss_analysis #1396

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
5fcd70f
Drop defunct susie_rss flags; add --rss-control to rss_analysis
Yining97 Jul 30, 2026
de8c651
Drop defunct susie_rss flags; add --rss-control; default r-mismatch=e…
Yining97 Jul 30, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
79 changes: 2 additions & 77 deletions code/SoS/mnm_analysis/mnm_methods/rss_analysis.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -133,59 +133,7 @@
"kernel": "SoS"
},
"outputs": [],
"source": [
"[global]\n",
"parameter: cwd = path('output')\n",
"parameter: modular_script_dir = path('code/script')\n",
"# --- per-study GWAS inputs (use either or both) ---------------------\n",
"parameter: gwas_meta = path('.')\n",
"parameter: gwas_tsv_list = [] # list of STUDY=PATH items\n",
"# --- region inputs (use either or both) -----------------------------\n",
"parameter: region_list = path('.')\n",
"parameter: regions = [] # list of chr:start-end strings\n",
"# --- LD reference + genome ------------------------------------------\n",
"parameter: ld_meta = path\n",
"parameter: genome = 'GRCh38'\n",
"# --- QC knobs (forwarded to gwas_sumstats_construct.R) --------------\n",
"parameter: qc_method = 'none' # none | slalom | dentist\n",
"parameter: impute = False\n",
"parameter: qc_args = '' # JSON object spliced into summaryStatsQc()\n",
"parameter: maf = 0.0025 # MAF cutoff (summaryStatsQc mafCutoff); 0 disables\n",
"parameter: skip_regions = [] # chr:start-end window(s) whose variants are dropped (skipRegion)\n",
"parameter: skip_analysis_pip_cutoff = 0.025 # skip a region below this max PIP (pipCutoffToSkip); 0 disables\n",
"parameter: allele_flip_kriging = False # kriging allele-flip QC: sign-flip switched z (logLR>2 & |z|>2); off by default\n",
"parameter: effective_n = True # case/control: use effective sample size 4/(1/n_case+1/n_control) as N (summaryStatsQc effectiveN); False -> raw N\n",
"# --- fine-mapping knobs (forwarded to fine_mapping.R) ---------------\n",
"parameter: methods = 'susie'\n",
"parameter: coverage = 0.95\n",
"parameter: secondary_coverage = '0.7,0.5'\n",
"parameter: min_abs_corr = 0.8\n",
"parameter: median_abs_corr = '' # empty -> off (OR-logic purity; needs pecotmr step-1)\n",
"parameter: pip_cutoff = 0.025\n",
"parameter: L = 20\n",
"parameter: L_greedy = 5\n",
"parameter: method_args = '' # nested per-method JSON object\n",
"# GWAS SuSiE-RSS fine-mapping: SER fallback is ON by default (reproduces the single-panel notebook):\n",
"# fit finite-sample R + EB LD-mismatch SuSiE-RSS and fall back to the single-effect (SER) result for\n",
"# regions susieR flags as unreliable. ser_fallback and r_mismatch are orthogonal: ser_fallback = False\n",
"# only disables the SER fallback (EB LD-mismatch stays on); pass r_mismatch = 'none' too for the\n",
"# pre-change plain multi-effect fit.\n",
"parameter: ser_fallback = True # fall back to single-effect (SER) when susieR flags R unreliable\n",
"parameter: r_finite = '' # finite-sample R size; empty -> auto (LD-panel sample size)\n",
"parameter: r_mismatch = 'eb' # LD-mismatch correction: 'eb' (default) or 'none'\n",
"parameter: r_mismatch_method = '' # rMismatch estimator 'mle'|'map'; empty -> pecotmr default\n",
"parameter: check_prior = '' # susie_rss check_prior 'TRUE'|'FALSE'; empty -> pecotmr default\n",
"# --- plot opt-out ---------------------------------------------------\n",
"parameter: no_plot = False\n",
"# --- output prefix for the manifest file ----------------------------\n",
"parameter: manifest_name = 'gwas_rss'\n",
"# --- infrastructure -------------------------------------------------\n",
"parameter: container = ''\n",
"parameter: job_size = 1\n",
"parameter: walltime = '2h'\n",
"parameter: mem = '16G'\n",
"parameter: numThreads = 1"
]
"source": "[global]\nparameter: cwd = path('output')\nparameter: modular_script_dir = path('code/script')\n# --- per-study GWAS inputs (use either or both) ---------------------\nparameter: gwas_meta = path('.')\nparameter: gwas_tsv_list = [] # list of STUDY=PATH items\n# --- region inputs (use either or both) -----------------------------\nparameter: region_list = path('.')\nparameter: regions = [] # list of chr:start-end strings\n# --- LD reference + genome ------------------------------------------\nparameter: ld_meta = path\nparameter: genome = 'GRCh38'\n# --- QC knobs (forwarded to gwas_sumstats_construct.R) --------------\nparameter: qc_method = 'none' # none | slalom | dentist\nparameter: impute = False\nparameter: qc_args = '' # JSON object spliced into summaryStatsQc()\nparameter: maf = 0.0025 # MAF cutoff (summaryStatsQc mafCutoff); 0 disables\nparameter: skip_regions = [] # chr:start-end window(s) whose variants are dropped (skipRegion)\nparameter: skip_analysis_pip_cutoff = 0.025 # skip a region below this max PIP (pipCutoffToSkip); 0 disables\nparameter: allele_flip_kriging = False # kriging allele-flip QC: sign-flip switched z (logLR>2 & |z|>2); off by default\nparameter: effective_n = True # case/control: use effective sample size 4/(1/n_case+1/n_control) as N (summaryStatsQc effectiveN); False -> raw N\n# --- fine-mapping knobs (forwarded to fine_mapping.R) ---------------\nparameter: methods = 'susie'\nparameter: coverage = 0.95\nparameter: secondary_coverage = '0.7,0.5'\nparameter: min_abs_corr = 0.8\nparameter: median_abs_corr = '' # empty -> off (OR-logic purity; needs pecotmr step-1)\nparameter: pip_cutoff = 0.025\nparameter: L = 20\nparameter: L_greedy = 5\nparameter: method_args = '' # nested per-method JSON object\n# GWAS SuSiE-RSS fine-mapping: SER fallback is ON by default (reproduces the single-panel notebook):\n# fit finite-sample R + EB LD-mismatch SuSiE-RSS and fall back to the single-effect (SER) result for\n# regions susieR flags as unreliable. ser_fallback and r_mismatch are orthogonal: ser_fallback = False\n# only disables the SER fallback (EB LD-mismatch stays on); pass r_mismatch = 'none' too for the\n# pre-change plain multi-effect fit. Requires susieR >= 0.16.6 (which moved R_mismatch_method /\n# check_prior into susie_rss_control(); pass those and other control settings via rss_control).\nparameter: ser_fallback = True # fall back to single-effect (SER) when susieR flags R unreliable\nparameter: r_finite = '' # finite-sample R size; empty -> auto (LD-panel sample size)\nparameter: r_mismatch = 'eb_mix' # LD-mismatch correction: 'none' | 'eb' | 'eb_mix' (residual-mixture EB, default)\nparameter: rss_control = '' # JSON object of susie_rss_control() settings, e.g. '{\"check_prior\":true,\"mismatch_estimator\":\"map\"}'; empty -> defaults\n# --- plot opt-out ---------------------------------------------------\nparameter: no_plot = False\n# --- output prefix for the manifest file ----------------------------\nparameter: manifest_name = 'gwas_rss'\n# --- infrastructure -------------------------------------------------\nparameter: container = ''\nparameter: job_size = 1\nparameter: walltime = '2h'\nparameter: mem = '16G'\nparameter: numThreads = 1"
},
{
"cell_type": "code",
Expand Down Expand Up @@ -227,30 +175,7 @@
"kernel": "SoS"
},
"outputs": [],
"source": [
"[gwas_fine_mapping]\n",
"# Per-RDS fan-out: one fine-mapping task per (study, region) GwasSumStats.\n",
"output: f\"{cwd}/fine_mapping/{_input:bnn}.gwas_finemap.rds\", group_by = 1\n",
"task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f\"{step_name}_{_output:bn}\"\n",
"bash: expand = '${ }', stderr = f\"{_output}.stderr\", stdout = f\"{_output}.stdout\", container = container\n",
" Rscript ${modular_script_dir}/pecotmr_integration/fine_mapping.R \\\n",
" --gwas-sumstats ${_input} \\\n",
" --methods ${methods} \\\n",
" --coverage ${coverage} \\\n",
" --secondary-coverage ${secondary_coverage} \\\n",
" --min-abs-corr ${min_abs_corr} \\\n",
" --pip-cutoff ${pip_cutoff} \\\n",
" --L ${L} \\\n",
" --L-greedy ${L_greedy} \\\n",
" ${('--median-abs-corr ' + str(median_abs_corr)) if str(median_abs_corr) != '' else ''} \\\n",
" ${('--method-args ' + repr(method_args)) if method_args else ''} \\\n",
" --ser-fallback ${'TRUE' if ser_fallback else 'FALSE'} \\\n",
" --r-mismatch ${r_mismatch} \\\n",
" ${('--r-finite ' + str(r_finite)) if str(r_finite) != '' else ''} \\\n",
" ${('--r-mismatch-method ' + r_mismatch_method) if r_mismatch_method else ''} \\\n",
" ${('--check-prior ' + check_prior) if check_prior else ''} \\\n",
" --output ${_output}"
]
"source": "[gwas_fine_mapping]\n# Per-RDS fan-out: one fine-mapping task per (study, region) GwasSumStats.\noutput: f\"{cwd}/fine_mapping/{_input:bnn}.gwas_finemap.rds\", group_by = 1\ntask: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f\"{step_name}_{_output:bn}\"\nbash: expand = '${ }', stderr = f\"{_output}.stderr\", stdout = f\"{_output}.stdout\", container = container\n Rscript ${modular_script_dir}/pecotmr_integration/fine_mapping.R \\\n --gwas-sumstats ${_input} \\\n --methods ${methods} \\\n --coverage ${coverage} \\\n --secondary-coverage ${secondary_coverage} \\\n --min-abs-corr ${min_abs_corr} \\\n --pip-cutoff ${pip_cutoff} \\\n --L ${L} \\\n --L-greedy ${L_greedy} \\\n ${('--median-abs-corr ' + str(median_abs_corr)) if str(median_abs_corr) != '' else ''} \\\n ${('--method-args ' + repr(method_args)) if method_args else ''} \\\n --ser-fallback ${'TRUE' if ser_fallback else 'FALSE'} \\\n --r-mismatch ${r_mismatch} \\\n ${('--r-finite ' + str(r_finite)) if str(r_finite) != '' else ''} \\\n ${('--rss-control ' + repr(rss_control)) if rss_control else ''} \\\n --output ${_output}"
},
{
"cell_type": "code",
Expand Down
36 changes: 19 additions & 17 deletions code/script/pecotmr_integration/fine_mapping.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -119,22 +119,19 @@ parser <- add_argument(parser, "--pip-cutoff-to-skip",
# fallback is ON by default (reproduces the single-panel notebook): fit a
# finite-sample R + EB LD-mismatch SuSiE-RSS and drop to the single-effect (SER)
# result for regions susieR flags as unreliable. These ride on gwas_args (GWAS
# mode only); rFinite/rMismatchMethod/checkPrior forward only when set, so the
# call also runs against a pecotmr that predates them.
# mode only); rFinite forwards only when set. susie_rss_control() settings
# (susieR >= 0.16.6) are passed as a JSON object via --rss-control.
parser <- add_argument(parser, "--ser-fallback",
help = "GWAS mode: TRUE/FALSE. Fall back to the single-effect (SER) result when susieR flags R unreliable (fineMappingPipeline serFallback). Default TRUE.",
type = "character", default = "TRUE")
parser <- add_argument(parser, "--r-finite",
help = "GWAS mode: finite-sample R correction size (fineMappingPipeline rFinite). Empty = auto (LD-panel sample size).",
type = "character", default = "")
parser <- add_argument(parser, "--r-mismatch",
help = "GWAS mode: LD-mismatch correction (fineMappingPipeline rMismatch): 'eb' (default) or 'none'.",
type = "character", default = "eb")
parser <- add_argument(parser, "--r-mismatch-method",
help = "GWAS mode: rMismatch estimator (fineMappingPipeline rMismatchMethod): 'mle' or 'map'. Empty = pecotmr default.",
type = "character", default = "")
parser <- add_argument(parser, "--check-prior",
help = "GWAS mode: TRUE/FALSE for susie_rss check_prior (fineMappingPipeline checkPrior). Empty = pecotmr default.",
help = "GWAS mode: LD-mismatch correction (fineMappingPipeline rMismatch): 'none', 'eb', or 'eb_mix' (residual-mixture EB, susieR >= 0.16.6). Default 'eb_mix'.",
type = "character", default = "eb_mix")
parser <- add_argument(parser, "--rss-control",
help = "GWAS mode: JSON object of susieR::susie_rss_control() settings (e.g. '{\"check_prior\":true,\"mismatch_estimator\":\"map\"}'), forwarded as fineMappingPipeline rssControl. Empty = susie_rss_control() defaults.",
type = "character", default = "")
# --- Multivariate / joint-fit knobs (QTL mode; mvsusie / fsusie). Each is
# opt-in and omitted from the pipeline call when left at its default, so this
Expand Down Expand Up @@ -317,18 +314,23 @@ if (has_gwas) {
ser_fallback <- as.logical(argv$ser_fallback)
if (is.na(ser_fallback))
stop("--ser-fallback must be TRUE or FALSE (got: ", argv$ser_fallback, ")")
# GWAS-only SuSiE-RSS knobs on top of the shared cs_args. rFinite /
# rMismatchMethod / checkPrior forward only when set (empty -> pecotmr default).
# GWAS-only SuSiE-RSS knobs on top of the shared cs_args. rFinite forwards
# only when set; --rss-control (JSON) becomes the rssControl named list of
# susie_rss_control() settings.
gwas_args <- c(cs_args,
list(serFallback = ser_fallback,
rMismatch = argv$r_mismatch))
if (nzchar(argv$r_finite)) gwas_args$rFinite <- as.numeric(argv$r_finite)
if (nzchar(argv[["r_mismatch_method"]]))
gwas_args$rMismatchMethod <- argv[["r_mismatch_method"]]
if (nzchar(argv$check_prior)) {
cp <- as.logical(argv$check_prior)
if (is.na(cp)) stop("--check-prior must be TRUE or FALSE (got: ", argv$check_prior, ")")
gwas_args$checkPrior <- cp
if (nzchar(argv$rss_control) && argv$rss_control != "." &&
argv$rss_control != "{}") {
rc <- tryCatch(jsonlite::fromJSON(argv$rss_control, simplifyVector = TRUE),
error = function(e) stop(
"--rss-control must be a JSON object (got: ", argv$rss_control,
"). Error: ", conditionMessage(e)))
if (!is.list(rc) || is.null(names(rc)) || any(!nzchar(names(rc))))
stop("--rss-control must be a JSON object with named fields, e.g. ",
'\'{"check_prior":true,"mismatch_estimator":"map"}\'.')
gwas_args$rssControl <- rc
}
res <- do.call(fineMappingPipeline, c(list(gss), gwas_args))
label <- paste0("GwasSumStats '", basename(argv$gwas_sumstats), "'")
Expand Down
Loading