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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, remove_indels = FALSE)

Arguments

sumstats

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

LD_data

A list containing combined LD variants data that is 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").

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.