qtl2helpers

_qtl2helpers.md

Helper functions to manipulate and/or coerce qtl2 objects. Eventually might make sense to submit as pull request?

add_pheno.R

#' Add phenotype data to a cross2 object
#'
#' @param x An object of class "cross2".
#' @param pheno A data.frame with phenotype data. All columns, apart from the one with
#' individual ID, will be converted to numeric values.
#' @param idcol A numeric or character value with the index or name of the column
#' that contains the individual IDs.
#' @param retain_all A logical value indicating whereas all individuals should be
#' retained in the cross2 object (default) or to only retain those that have
#' both genotype and phenotype data.
#'
#' @export
#' @rdname add_pheno
add_pheno <- function(x, pheno, idcol = 1L, retain_all = TRUE){
  UseMethod("add_pheno")
}

#' @export
#' @rdname add_pheno
add_pheno.cross2 <- function(x, pheno, idcol = 1L, retain_all = TRUE){
  
  #### Format pheno data.frame ####
  
  # Coerce to data.frame (in case tibble or data.table is provided)
  pheno <- as.data.frame(pheno)
  
  # Get column name
  # if it is provided as a character
  if(is.character(idcol)){
    idcol <- which(colnames(pheno) %in% idcol)
    if(length(idcol) == 0) stop("No ID column found with that name.")
  }
  if(length(idcol) != 1) stop("Only 1 ID column can be provided.")
  
  # Get vector of individual IDs in phenotype provided
  ids <- as.character(pheno[[idcol]])
  
  # remove ID column from pheno table
  pheno <- pheno[, -idcol]
  pheno <- as.matrix(pheno) # ensure it's matrix

  # Add these to rownames of phenotype table
  rownames(pheno) <- ids
  
  # If user does not want to retain all data
  if(!retain_all){
    # Retain only those individuals that are in the cross object
    ids <- ids[which(ids %in% rownames(x$geno[[1]]))]
    
    # Subset phenotype table to retain only those individuals
    pheno <- pheno[ids, ]
  } 
  
  # Convert to matrix using qtl2 helper function
  pheno <- qtl2:::pheno2matrix(pheno)
  
  
  #### Add to cross2 object ####
  
  # If user does not want to retain all data
  if(!retain_all){
    # Subset cross2 object to retain only IDs in phenotype file
    x <- x[rownames(pheno), ]
  }
  
  # Add pheno slot
  x[["pheno"]] <- pheno
  
  return(x)
}

wrapped into a package along with other "tidiers": https://github.com/tavareshugo/qtl2helper