Run QC on a SumStats Collection — summaryStatsQc • pecotmr

Applies a single QC pass to a QtlSumStats or GwasSumStats collection: per-row sanity checks via .applySanityChecks (drop rows with out-of-range / zero P, BETA == 0, SE <= 0, NA in vital columns; clamp tiny P; normalize CHR; coerce signed columns to numeric), variant-content filters (MAF / INFO / N) via .applyContentFilters, optional skipRegion drop, optional PIP screen, panel-vs-sumstats allele harmonization against the ldSketch via harmonizeAlleles (which handles indels, strand-ambiguous variants, sign / strand flips, and duplicate drops in a single sweep), optional SLALOM/DENTIST LD-mismatch QC, and optional RAISS imputation. No Bioconductor genome / dbSNP packages required.

Usage

summaryStatsQc(
  sumstats,
  removeIndels = FALSE,
  removeStrandAmbiguous = TRUE,
  mafCutoff = 0,
  infoCutoff = 0,
  nCutoff = 5,
  keepVariants = NULL,
  skipRegion = NULL,
  pipCutoffToSkip = 0,
  zMismatchQc = c("none", "slalom", "dentist"),
  alleleFlipKriging = FALSE,
  effectiveN = TRUE,
  impute = FALSE,
  imputeOpts = list(rcond = 0.01, r2Threshold = 0.6, minimumLd = 5, lamb = 0.01),
  matchMinProp = 0,
  coerceNumeric = TRUE,
  normalizeChr = TRUE,
  dropNonstandardChr = TRUE,
  dropMissData = TRUE,
  dropPOutOfRange = TRUE,
  clampSmallP = TRUE,
  smallPFloor = 4.94065645841247e-324,
  dropZeroEffect = TRUE,
  dropNonpositiveSe = TRUE
)

Arguments

sumstats: A QtlSumStats or GwasSumStats collection.
removeIndels: Logical (length 1). When TRUE, drop indels during panel harmonization. Default FALSE.
removeStrandAmbiguous: Logical (length 1). When TRUE, drop A/T and C/G strand-ambiguous variants. Default TRUE.
mafCutoff: Numeric (length 1). MAF threshold (variants with MAF < mafCutoff are dropped). Default 0. Requires MAF or FRQ column when non-zero.
infoCutoff: Numeric (length 1). INFO score threshold. Default 0. Requires INFO column when non-zero.
nCutoff: Numeric (length 1). Sample-size deviation threshold: drop variants whose N is more than nCutoff median-absolute-deviations from the median. Set to 0 to disable. Default 5.
keepVariants: Optional character vector of variant IDs (SNP column) to retain prior to harmonization.
skipRegion: Optional character vector of "chr:start-end" strings, or a GRanges, of regions to drop.
pipCutoffToSkip: Numeric (length 1). When != 0, run an LD-independent single-effect SER screen and skip the entry if no PIP exceeds the cutoff. < 0 resolves to 3 / nVariants. Default 0 (no screen).
zMismatchQc: One of "none" (default), "slalom", "dentist".
alleleFlipKriging: Logical (length 1). Opt-in kriging LD-consistency prefilter run before SLALOM/DENTIST. Default FALSE.
effectiveN: Logical (length 1). When TRUE (default) and the input carries case/control counts — per-variant N_CASE / N_CONTROL mcols, else the study-level nCase / nControl scalars — the working per-variant N is set to the effective sample size effectiveN(nCase, nControl) BEFORE the N-cutoff filter, so the filter, kriging, and the downstream fit all use N_eff. When both counts and an N column are present the counts win: N is overridden and the override is logged. Inputs with no counts (quantitative traits) are unchanged. The escape hatch effectiveN = FALSE restores the raw N column (or, when there is no N, the raw total nCase + nControl) with no override. qcInfo$options$effectiveN records the setting and each entry's nSource is one of "effective", "column", "total", or NA.
impute: Logical (length 1). Run RAISS imputation against the ldSketch. Default FALSE. (Note: RAISS against the sketch is not yet fully wired for the new path; the option is accepted but currently emits a warning and is skipped.)
imputeOpts: Named list of RAISS parameters.
matchMinProp: Minimum proportion of LD panel variants that must be matched by the sumstats; default 0.
coerceNumeric: Logical. Coerce signed columns (Z/BETA/SE/OR/LOG_ODDS/SIGNED_SUMSTAT/P/MAF/FRQ/INFO/N) to numeric. Default TRUE.
normalizeChr: Logical. Strip "chr" prefix, uppercase the chromosome label, and map 23->X, 24->Y, M->MT. Default TRUE.
dropNonstandardChr: Logical. Drop variants whose CHR (after normalization) is outside 1..22, X, Y, MT. Default TRUE.
dropMissData: Logical. Drop rows with NA in any vital column (chrom, pos, A1, A2, and at least one of Z / BETA). Default TRUE.
dropPOutOfRange: Logical. Drop rows where P < 0 or P > 1. Default TRUE.
clampSmallP: Logical. Floor non-negative P values below smallPFloor to smallPFloor so -log10(P) stays finite. Applied to both input and Z-derived P values. Default TRUE.
smallPFloor: Numeric (length 1). Floor for clampSmallP. Default 5e-324 (R's smallest positive double).
dropZeroEffect: Logical. Drop rows where any effect column is exactly 0 (BETA, LOG_ODDS, SIGNED_SUMSTAT) or OR is exactly 1. Default TRUE.
dropNonpositiveSe: Logical. Drop rows where SE <= 0. Default TRUE.

Value

A new QtlSumStats / GwasSumStats with cleaned entries and qcInfo populated.

Details

The returned collection has its qcInfo slot populated with a per-entry audit record (variant counts, drop counts at each step, which filters fired, etc.). Fine-mapping and TWAS-weights pipelines reject SumStats inputs where length(getQcInfo(x)) == 0L.

Column-availability error contract: a non-zero mafCutoff requires every entry to carry a MAF column; non-zero infoCutoff requires INFO; non-zero nCutoff requires N. Missing column with a non-zero cutoff is a hard error.