Load a GwasSumStats collection from a manifest — loadGwasSumStatsFromManifest • pecotmr

Build a GwasSumStats from a manifest with one row per study. No QC is run (the result carries qcInfo = list()).

Usage

loadGwasSumStatsFromManifest(
  manifest,
  genome = NULL,
  ldSketch = NULL,
  region = NULL,
  minLdOverlapWarn = 0.5,
  columnMapping = NULL,
  sampleSelect = NULL,
  formatMapping = NULL
)

Arguments

manifest: A data.frame or path. Columns (snake_case aliases accepted): study (required, unique), sumStatsPath (required), columnMapping (optional), nCase / nControl (optional), varY (optional), and the single-valued genome / ldSketchPath.
genome: Genome build; reconciled with a genome column.
ldSketch: A GenotypeHandle or a spec (path/prefix/genoMeta); reconciled with an ldSketchPath column.
region: Optional chr:start-end string, GRanges, or one-row data.frame restricting the variants read (honoured only for tabix-indexed text and bgzipped+tabixed VCF; ignored with a warning otherwise).
minLdOverlapWarn: Warn when the fraction of sumstats variants present in the LD sketch falls below this (default 0.5).
columnMapping: Optional default column mapping (a named list/vector, or a path to a YAML file of standardName: sourceName entries) applied when a row has no columnMapping.
sampleSelect: Optional GWAS-VCF FORMAT sample (study) column to read.
formatMapping: Optional GWAS-VCF FORMAT tag mapping (canonical stat -> FORMAT field), overriding ES/SE/LP/SS/EAF defaults.

Value

A GwasSumStats object.