Skip to contents

sLDSC Postprocessing Pipeline

Source: R/sldscPostprocessingPipeline.R
sldscPostprocessingPipeline.Rd

Postprocess polyfun's per-trait sLDSC outputs (already loaded into an SldscData object) into a single results object with per-trait tau*, EnrichStat with back-solved jackknife SE, and a DerSimonian-Laird random-effects meta-analysis across traits. All file I/O is done up front by the reader functions (readSldscAnnot, readSldscFrq, readSldscTrait); this pipeline is pure computation over the in-memory SldscData.

Usage

sldscPostprocessingPipeline(
  sldscData,
  mafCutoff = 0.05,
  targetCategories = NULL,
  targetLabels = NULL
)

Arguments

sldscData

An SldscData object bundling the annotation table, the reference-panel allele frequencies, and the per-trait single/joint polyfun runs.

mafCutoff

Numeric MAF cutoff applied via the object's frq table. Default 0.05. Set to 0 to opt out (requires frq data when > 0).

targetCategories

Optional character vector of target annotation names to retain. Auto-detected from the joint run (or first single run) when NULL.

targetLabels

Optional display names, same length / order as targetCategories, applied to every output column / tau* block colname.

Value

A list with per_trait (per-trait standardised tables), meta tables (tauStar, enrichment, enrichstat), and a params record of the call options.

See also

SldscData, readSldscAnnot, readSldscFrq, readSldscTrait