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Run MAGMA gene-based analysis

Source: R/magmar.R
magmar.Rd

This function provides a wrapper to MAGMA, which performs gene-based testing from GWAS summary statistics. Details of MAGMA described in de Leeuw et al. (PLoS Cumputational Biology 2015; https://doi.org/10.1371/journal.pcbi.1004219). The MAGMA binary and reference files are available from the Complex Trait Genetics lab (https://ctg.cncr.nl/software/magma).

Usage

magmar(
  sumstats_df,
  pval_col = p_value,
  snp_col = rsid,
  samplesize_col = samplesize,
  magma_bin,
  bfile,
  gene_file,
  out_file
)

Arguments

sumstats_df

Dataframe containing GWAS summary statistics

pval_col

Column containing p-values

snp_col

Column containing rsids

samplesize_col

Column containing sample size

magma_bin

Path to MAGMA binary

bfile

Path to reference data in plink bfile format (path should not include the extensions)

gene_file

Path to file containing gene locations

out_file

Output directory + file prefix

Value

Path to MAGMA results file

See also

Other Gene-based testing: s_multixcan(), s_predixcan()

Examples

if (FALSE) {
magmar(sumstats_df, magma_bin = "/path/to/magma", bfile = "/path/to/bfiles", gene_file = "/path/to/genes", out_file = "magma_output")
}