R/getGroupsFromDesign.R

In ryananeff/superNOVA: Differential coexpression within multiple subgroups of data

#' @title Split input matrix(es) based on the design matrix.
#' @description This function splits the input matrix(es) based on a design matrix, into a named list of subsetted matrices. If the design matrix has no names, this function will create names for the resulting list of matrices.
#' @param inputMat Input (e.g., expression) matrix which will be subsetted.
#' @param inputMatB Optional input (e.g., expression) matrix which will be subsetted in the same way.
#' @param design Standard design matrix, must specify at least two conditions. For more info, see ?model.matrix
#' @param secondMat Logical value indicating whether there is a second input matrix to be subsetted.
#' @return A list whose first element is a list of subsetted matrices and whose second element is a list of group names.
#' @examples
#' data(darmanis); data(design_mat); darmanis_subset = darmanis[1:30, ]
#' groups_from_design = getGroupsFromDesign(inputMat = darmanis_subset, design = design_mat)
#' str(groups_from_design)
#' @export
getGroupsFromDesign <- function(inputMat, design, inputMatB = NULL, secondMat = FALSE){

  nGroups = qr(design)$rank

  if(nGroups <= 1) stop("Design matrix must specify at least 2 conditions.")

  listGroupMats = list()
  listGroupNames = list()

  #if the design matrix is not named, assign it basic names
  if(!is.character(colnames(design))){
    colnames(design) = toupper(letters[1:ncol(design)])
  }

  if(!secondMat){
    for(i in 1:nGroups){
      tmpCols = as.numeric(which(design[,i] == 1))
      listGroupMats[[i]] = inputMat[ , tmpCols, drop = FALSE]
      listGroupNames[[i]] = colnames(design)[i]
    }
    return(list(listGroupMats, listGroupNames))
  } else {
    listGroupMatsB = list()
    for(i in 1:nGroups){
      tmpCols = as.numeric(which(design[,i] == 1))
      listGroupMats[[i]] = inputMat[ , tmpCols, drop = FALSE]
      listGroupMatsB[[i]] = inputMatB[, tmpCols, drop = FALSE]
      listGroupNames[[i]] = colnames(design)[i]
    }
    return(list(listGroupMats, listGroupMatsB, listGroupNames))
  }
}