Summarize GWAS summary statistics

Opens one or more parquet files as an Arrow dataset, computes per-file summary statistics (SNP count, EAF range, median SE, etc.), and appends binary-trait columns (n_cases, n_controls, n_effective) when trait_type = "binary".

Usage

summarize_sumstats(
  parquet_files,
  trait_type,
  min_mac = 100,
  se_col = SE,
  beta_col = B,
  eaf_col = EAF,
  chr_col = CHR,
  pos_col = POS_38,
  rsid_col = RSID,
  n_col = N,
  effective_n_col = EffectiveN,
  case_n_col = CaseN,
  control_n_col = ControlN
)

Arguments

parquet_files

Character vector of paths to parquet files.

trait_type

"binary" or "quantitative" (required).

min_mac

Minimum minor allele count filter. Default 100.

se_col

Bare column name for SE. Default SE.

beta_col

Bare column name for effect size. Default B.

eaf_col

Bare column name for effect allele frequency. Default EAF.

chr_col

Bare column name for chromosome. Default CHR.

pos_col

Bare column name for position. Default POS_38.

rsid_col

Bare column name for rsid. Default RSID.

n_col

Bare column name for total N. Default N.

effective_n_col

Bare column name for effective N. Default EffectiveN.

case_n_col

Bare column name for case N. Default CaseN.

control_n_col

Bare column name for control N. Default ControlN.

Value

A tibble::tibble() with one row per file and summary columns.

Details

Summarize GWAS summary statistics files

Examples

if (FALSE) { # \dontrun{
summary <- summarize_sumstats(
  parquet_files = c("study1.parquet", "study2.parquet"),
  trait_type    = "binary"
)
} # }