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Preprocess input data for RSS analysis

Source: R/sumstats_qc.R
rss_basic_qc.Rd

This function preprocesses summary statistics and LD data for RSS analysis. It performs allele quality control, flipping alleles as necessary, and removes specified regions from the analysis.

Usage

rss_basic_qc(
  sumstats,
  LD_data,
  skip_region = NULL,
  keep_indel = TRUE,
  return_LD_mat = TRUE
)

Arguments

sumstats

A data frame containing summary statistics with columns "chrom", "pos", "A1", and "A2".

LD_data

An LDData S4 object or a legacy list containing combined LD variants data, as generated by load_LD_matrix.

skip_region

A character vector specifying regions to be skipped in the analysis (optional). Each region should be in the format "chrom:start-end" (e.g., "1:1000000-2000000").

return_LD_mat

Logical; if FALSE, return only harmonized summary statistics and skip LD-matrix subsetting. This is useful when the reference input is genotype-backed X_ref. Defaults to TRUE for backwards compatibility.

Value

A list containing the processed summary statistics and LD matrix. - sumstats: A data frame containing the processed summary statistics. - LD_mat: The processed LD matrix.