read_plink_assoc_file: Read a PLINK '.assoc' file

In richelbilderbeek/plinkr: Interface to PLINK

Read a PLINK .assoc file

Description

Read a PLINK .assoc file

Usage

read_plink_assoc_file(assoc_filename)

Arguments

assoc_filename

name of a PLINK .assoc file. Use read_plink_assoc_file to read a PLINK .assoc file.

Value

a tibble.

The tibble has these columns:

a tibble with the following columns:

• CHR: Chromosome number

• SNP: SNP identifier

• BP: Physical position (base-pair)

• A1: Minor allele name (based on whole sample)

• F_A: Frequency of this allele in cases

• F_U: Frequency of this allele in controls

• A2: Major allele name

• CHISQ: Basic allelic test chi-square (1df)

• P: Asymptotic p-value for this test

• OR: Estimated odds ratio (for A1, i.e. A2 is reference)

• SE: Standard error of the estimated log(odds ratio)

• L95: Lower bound of the 95% confidence interval of the odds ratio

• U95: Upper bound of the 95% confidence interval of the odds ratio

The table with have as much rows as the number of SNPs

Note that parameters in uppercase are named as such by PLINK.

Author(s)

Richèl J.C. Bilderbeek

Examples

read_plink_assoc_file(
  assoc_filename = get_plinkr_filename("run1.assoc")
)

richelbilderbeek/plinkr documentation built on March 25, 2024, 3:18 p.m.