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Format MR results for forest plot

Source: R/forest_plot2.R
format_mr_results.Rd

This function takes the results from mr() and is particularly useful if the MR has been applied using multiple exposures and multiple outcomes. It creates a new data frame with the following:

  • Variables: exposure, outcome, category, outcome sample size, effect, upper ci, lower ci, pval, nsnp

  • only one estimate for each exposure-outcome

  • exponentiated effects if required

Usage

format_mr_results(
  mr_res,
  exponentiate = FALSE,
  single_snp_method = "Wald ratio",
  multi_snp_method = "Inverse variance weighted",
  ao_slc = TRUE,
  priority = "Cardiometabolic"
)

Arguments

mr_res

Results from mr().

exponentiate

Convert effects to OR? The default is FALSE.

single_snp_method

Which of the single SNP methods to use when only 1 SNP was used to estimate the causal effect? The default is "Wald ratio".

multi_snp_method

Which of the multi-SNP methods to use when there was more than 1 SNPs used to estimate the causal effect? The default is "Inverse variance weighted".

ao_slc

Logical; retrieve sample size and subcategory using available_outcomes(). If set to FALSE mr_res must contain the following additional columns: subcategory and sample_size.

priority

Name of category to prioritise at the top of the forest plot. The default is "Cardiometabolic".

Value

data frame.

Details

By default it uses the available_outcomes() function to retrieve the study level characteristics for the outcome trait, including sample size and outcome category. This assumes the MR analysis was performed using outcome GWAS(s) contained in MR-Base.

If ao_slc is set to TRUE then the user must supply their own study level characteristics. This is useful when the user has supplied their own outcome GWAS results (i.e. they are not in MR-Base).