GWAS.df.example: GWAS data

Description Usage Format

Description

A dataset containing GWAS data

Usage

1

Format

Dataframe, one row per SNP, with 6 columns (PLINK –logistic/–linear output format)

CHR

Chromosome for SNP (sex chromosomes coded numerically). Data type: integer

POS

Chromosomal position for each SNP, in base pairs. Data type: integer

SNP

Variant ID (such as dbSNP ID "rs..."). Data type: character Note: Must be the same naming scheme as used in eQTL.df to ensure proper matching.

P

p-value for the SNP from GWAS analysis. Data type: numeric

BETA

beta for the SNP from GWAS analysis. Data type: numeric

P

OPTIONAL Name of the phenotype for which the GWAS data refers. Data type: character This column is optional and is useful if your GWAS.df contains data for multiple phenotypes, such as one might obtain from a PheWAS. If GWAS.df does not contain a PHE column, eQTpLot will assume all the supplied GWAS data is for a single phenotype, with a name to be specified with the trait argument.


RitchieLab/eQTpLot documentation built on April 29, 2021, 8:21 p.m.