R/metaPvalues.R

In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

#' @title Meta-analysis of p-values
#' 
#' @description Performs meta-analys of pvalues using the sum of logs method (Fisher's method)
#'
#' @param x a \code{dsOmics} object obtained from \code{ds.limma}, \code{ds.GWAS} or \code{ds.PLINK} functions applied o 2 or more studies
#' 
#' @return a matrix with features p-values of each study and its combination 
#' 
#' @author Gonzalez, JR.
#'
#' @export
#' @importFrom magrittr %>%
#' @importFrom tibble add_column
#' @import dplyr
#' @import metap 

metaPvalues <- function(x){
  
  if(length(x)==1)
    stop('Nothing to be meta-analyzed. There is only a single study')


  if (inherits(x, 'dsLimma')){
    ff <- function(x, y){
      inner_join(x, y, 
                 by='id')
    }
    jj <- 'id|P.Value'
  } else if (inherits(x, 'dsGWAS')){
    ff <- function(x, y){
      inner_join(x, y, 
                 by=c('rs', 'chr', 'pos'))
    }
    jj <- 'rs|chr|pos|p.value'
  } else{
      stop("Object should be of class 'dsLimma', 'dsOmics' or 'dsPLINK' ")
  }

  pvals <- Reduce(ff, x)
  ii <- grep(jj, colnames(pvals))
  pvals <- pvals[,ii]
  if (inherits(x, 'dsLimma')){
    colnames(pvals)[-1] <- names(x)
    p.meta <- unlist(apply(pvals[,-1], 1, function(x) metap::sumlog (x)$p))
  } else if (inherits(x, 'dsGWAS')) {
    colnames(pvals)[-c(1:3)] <- names(x)
    p.meta <- unlist(apply(pvals[,-c(1:3)], 1, function(x) metap::sumlog (x)$p))
  }
  
  ans <- tibble::add_column(pvals, p.meta=p.meta)%>%arrange(p.meta)
  
  return(ans)
}