analysis_association: Run association analysis

In FireGutter/geneference: Simulating and analysing genes with LT-FH

Description

Calls PLINK to run an association analysis on specified data.

Usage

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.

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().

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.

FireGutter/geneference documentation built on Dec. 17, 2021, 8:27 p.m.