R/format_radial.R

In WSpiller/MRPracticals: An R Package illustrating features of MR Base and RadialMR

#' format_radial
#'
#' Reads in summary data. Checks and organises columns for use in calculating radial IVW and radial MR-Egger estimates. Where variant IDs are not provided, a vector is generated for variant identification.
#'
#' @param BXG A numeric vector of beta-coefficient values for genetic associations with the first variable (exposure).
#' @param BYG A numeric vector of beta-coefficient values for genetic associations with the second variable (outcome).
#' @param seBXG The standard errors corresponding to the beta-coefficients \code{BXG}.
#' @param seBYG The standard errors corresponding to the beta-coefficients \code{BYG}.
#' @param RSID A vector of names for genetic variants included in the analysis. If variant IDs are not provided (\code{RSID="NULL"}), a vector of ID numbers will be generated.
#' @return A formatted data frame.
#' 
#'@author Wes Spiller; Jack Bowden.
#'@references Bowden, J., et al., Improving the visualization, interpretation and analysis of two-sample summary data Mendelian randomization via the Radial plot and Radial regression. International Journal of Epidemiology, 2018. 47(4): p. 1264-1278.
#'@export
#'@examples
#'
#' format_radial(summarydata[,1],summarydata[,3],summarydata[,2],summarydata[,4])
#' 

#Function for formatting data frame

format_radial<-function(BXG,BYG,seBXG,seBYG,RSID){
  
  #Generates placeholder SNP IDs if not provided.
  
  if(missing(RSID)) {
    RSID<-seq(from=1,to=length(BYG),by=1)
    
    warning("Missing SNP IDs; Generating placeholders")
  } 
  
  #Rearrange variable order in formatted data frame
  F.Data<-data.frame(RSID,BXG,BYG,seBXG,seBYG)
  
  #Rename variables based on MRBase conventional names
  names(F.Data)<-c("SNP","beta.exposure","beta.outcome","se.exposure","se.outcome")
  
  return(F.Data)
}