Create a configuration file for METAL

This function can be used to generate a configuration for METAL, a tool for performing meta-analysis of GWAS summary statistics https://github.com/statgen/METAL. The file created by this function can be used to run a meta-analysis. Details of the arguments to METAL are described in the METAL documentation: https://genome.sph.umich.edu/wiki/METAL_Documentation.

Usage

metal_config(
  config_name,
  output_dir,
  study_files,
  SCHEME = "STDERR",
  AVERAGEFREQ = "ON",
  MINMAXFREQ = "OFF",
  TRACKPOSITIONS = "ON",
  MARKERLABEL = "MARKER",
  CHROMOSOMELABEL = "CHROM",
  POSITIONLABEL = "POS",
  EFFECT_ALLELE = "EFFECT_ALLELE",
  OTHER_ALLELE = "OTHER_ALLELE",
  EFFECTLABEL = "BETA",
  STDERR = "SE",
  FREQLABEL = "EAF",
  NCASE = NULL,
  NCONTROL = NULL,
  SAMPLESIZE = NULL
)

Arguments

config_name

(string) Name of the configuration

output_dir

(path) Path to output directory where GWAS meta-analysis data should be stored

study_files

(vector) Character vector of paths to summary statistics that should be included in the GWAS

SCHEME

(string) Either "SAMPLESIZE" or "STDERR" (default), corresponding to the METAL analysis scheme

AVERAGEFREQ

(string) Either "ON" (default) or "OFF", allowing METAL to report the mean effect allele frequency across files

MINMAXFREQ

(string) Either "ON" (default) or "OFF", allowing METAL to report the min/max effect allele frequency across files

TRACKPOSITIONS

(string) Either "ON" (default) or "OFF", allowing METAL to report chromosome/position in the output

MARKERLABEL

(string) Column containing unique markers to analyze (this column must be named the same across all input files)

CHROMOSOMELABEL

(string) Column containing chromosomes (this column must be named the same across all input files)

POSITIONLABEL

(string) Column containing genomic positions (this column must be named the same across all input files)

EFFECT_ALLELE

(string) Column containing effect alleles (this column must be named the same across all input files)

OTHER_ALLELE

(string) Column containing non-effect alleles (this column must be named the same across all input files)

EFFECTLABEL

(string) Column containing effect sizes corresponding to the effect allele (this column must be named the same across all input files)

STDERR

(string) Column containing standard errors fo the effect estimate (this column must be named the same across all input files)

FREQLABEL

(string) Column containing effect allele frequencies (this column must be named the same across all input files)

NCASE

(string) Column containing number of cases (this column must be named the same across all input files)

NCONTROL

(string) Column containing number of controls (this column must be named the same across all input files)

SAMPLESIZE

(string) Column containing total samplesize (this column must be named the same across all input files)

Value

Path to METAL configuration file

See also

Run GWAS meta-analysis using METAL: metal_run()

Other GWAS meta-analysis: metal_run(), mr_mega()

Examples

if (FALSE) {
metal_config(config_name = "name-of-analysis", output_dir = "/path/to/output/", study_files = c("/path/to/sumstats_1.txt", "/path/to/sumstats_2.txt"))
}