MR object — MR • genepi.utils

An MR object is a container for vectors and matrices of 2 or more GWAS data.

Usage

MR(
  exposure,
  outcome,
  harmonise_strictness = 2,
  correlation = NULL,
  verbose = TRUE
)

exposure: a GWAS object or list of GWAS objects
outcome: a GWAS object
harmonise_strictness: an integer (1,2,3) corresponding to the TwoSampleMR harmonisation options of the same name.
correlation: a matrix, correlation matrix of signed R values between variants
verbose: a logical, print more information

an S7 class genepi.utils::MR object

snps: character, variant ID
chr: character, chromosome identifier
bp: integer, base position
ea: character, effect allele
oa: character, other allele
eafx: numeric, exposure effect allele frequency
nx: integer, exposure total number of samples
ncasex: integer, exposure number of cases
bx: numeric, exposure effect size
bxse: numeric, exposure effect size standard error
px: numeric, exposure p-value
eafy: numeric, exposure effect allele frequency
ny: integer, exposure total number of samples
ncasey: integer, exposure number of cases
by: numeric, exposure effect size
byse: numeric, exposure effect size standard error
py: numeric, exposure p-value
exposure_id: character, the GWAS identifier
exposure: character, the GWAS exposure
outcome_id: character, the GWAS identifier
outcome: character, the GWAS outcome
group: integer, grouping variable used for plotting
index_snp: logical, whether the variant is an index variant (via clumping)
proxy_snp: character, the id of the proxy snp
ld_info: logical, whether there is LD information
info: data.frame, information about the loaded GWAS objects
correlation: matrix, a correlation matrix of signed R values between variants