R/lump.R

In yeswzc/LUMP: What the Package Does (One Line, Title Case)

#' @export
lump = function(betas, sample_in_row = "N"){
      #betas: matrix/data.frame if 
      #columns as probe IDs and row as samples: sample_in_row = Y
      #else sample_in_row = "N
      if(sample_in_row == "Y"){
         betas = betas[,colnames(betas) %in% lump_cpg, drop=F]
         lump_purity = apply(betas, MARGIN = 1, function(x){ LUMP = min(1, mean(x)/0.85); LUMP})
     }else{
         betas = betas[rownames(betas) %in% lump_cpg,, drop=F]
         lump_purity = apply(betas, MARGIN = 2, function(x){ LUMP = min(1, mean(x)/0.85); LUMP})
     }
     return(lump_purity)
}