mapStat: Map marker summary statistics to Glist

In psoerensen/qgg: Statistical Tools for Quantitative Genetic Analyses

Map marker summary statistics to Glist

Description

Quality control is a critical step for working with summary statistics (in particular for external). Processing and quality control of GWAS summary statistics includes:

- map marker ids (rsids/cpra (chr, pos, ref, alt)) to LD reference panel data

- check effect allele (flip EA, EAF, Effect)

- check effect allele frequency

- thresholds for MAF and HWE

- exclude INDELS, CG/AT and MHC region

- remove duplicated marker ids

- check which build version

- check for concordance between marker effect and LD data

Usage

mapStat(
  Glist = NULL,
  stat = NULL,
  excludeMAF = 0.01,
  excludeMAFDIFF = 0.05,
  excludeINFO = 0.8,
  excludeCGAT = TRUE,
  excludeINDEL = TRUE,
  excludeDUPS = TRUE,
  excludeMHC = FALSE,
  excludeMISS = 0.05,
  excludeHWE = 1e-12
)

Arguments

Glist	list of information about genotype matrix stored on disk
stat	dataframe with marker summary statistics
excludeMAF	exclude marker if minor allele frequency (MAF) is below threshold (0.01 is default)
excludeMAFDIFF	exclude marker if minor allele frequency difference (MAFDIFF) between Glist$af and stat$af is above threshold (0.05 is default)
excludeINFO	exclude marker if info score (INFO) is below threshold (0.8 is default)
excludeCGAT	exclude marker if alleles are ambigous (CG or AT)
excludeINDEL	exclude marker if it an insertion/deletion
excludeDUPS	exclude marker id if duplicated
excludeMHC	exclude marker if located in MHC region
excludeMISS	exclude marker if missingness (MISS) is above threshold (0.05 is default)
excludeHWE	exclude marker if p-value for Hardy Weinberg Equilibrium test is below threshold (0.01 is default)

Author(s)

Peter Soerensen

psoerensen/qgg documentation built on March 9, 2024, 10:02 p.m.