Run association analysis

Calls PLINK to run an association analysis on specified data.

analysis_association(
  geno_file,
  pheno_file,
  pheno_name,
  out_dir,
  bed = TRUE,
  plink_path = TRUE
)

Arguments

geno_file	string specifying path to genotypes file, including file extension.
pheno_file	string specifying path to phenotypes file, including file extension.
pheno_name	column name of phenotype to be used in analysis.
out_dir	directory to save results in, including "/" or "\\" at the end.
bed	logical indicating whether or not the genotypes file is a .bed file. FALSE if the file is .ped.
plink_path	TRUE if user has added PLINK to the system variable "PATH". Otherwise a string specifying the path to the folder containing plink.exe.

Value

Does not return anything, but PLINK writes its results to disk in out_dir. The name of the written file depends on pheno_name:

• pheno: output filename is "GWAS".

• line_pheno: output filename is "linear".

• LTFH_pheno: output filename is "LTFH".

• GWAX_pheno: output filename is "GWAX".

The file format of the written file and the columns contained in it depends on which phenotype is used for the analysis.

Details

PLINK uses the pheno_name column to determine which kind of analysis to run on the data.

• Use "pheno" for a 1 degree of freedom chi-square test with the case-control representation of the phenotype.

• Use "line_pheno" for a linear regression using the case-control representation of the phenotype.

• Use "LTFH_pheno" for a linear regression using the LTFH phenotype. Requires that pheno_file was created/edited by assign_ltfh_phenotype().

• Use "GWAX_pheno" for a linear regression using the LTFH phenotype. Requires that pheno_file was created/edited by assign_GWAX_phenotype().