Load a QtlSumStats collection from a manifest — loadQtlSumStatsFromManifest • pecotmr

Build a QtlSumStats from a manifest with one row per (study, context, trait) tuple. No QC is run.

Usage

loadQtlSumStatsFromManifest(
  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, context, trait (required), sumStatsPath (required), columnMapping (optional), varY (optional), and the single-valued genome / ldSketchPath.
genome: Genome build; reconciled with a genome column.
ldSketch: A GenotypeHandle or spec; reconciled with an ldSketchPath column.
region, minLdOverlapWarn, columnMapping, sampleSelect, formatMapping: As for loadGwasSumStatsFromManifest.

Value

A QtlSumStats object.