R/get_qsvs.R

In LieberInstitute/qsvaR: Generate Quality Surrogate Variable Analysis for Degradation Correction

#' Generate matrix of qsvs
#'
#'  Using the pcs and the k number of components be included,
#'  we generate the qsva matrix.
#'
#'
#' @param qsvPCs prcomp object generated by taking
#' the pcs of degraded transcripts
#' @param k number of qsvs to be included.
#'
#' @return matrix with k principal components for each sample.
#' @export
#'
#' @examples
#' qsv <- getPCs(rse_tx, "tpm")
#' get_qsvs(qsv, 2)
get_qsvs <- function(qsvPCs, k) {
  
  #Validate qsvPCs is a prcomp object
  if (!is(qsvPCs, "prcomp")) {
    stop("'qsvPCs' must be a prcomp object.", call. = FALSE)
  }

  # check that k isn't zero
  if (k <= 0 | k > ncol(qsvPCs$x)) {
    stop(paste("k must between 1 and",ncol(qsvPCs$x)))
  }
  
  qSVs <- qsvPCs$x[, seq_len(k), drop = FALSE]
  colnames(qSVs) <- paste0("qSV", seq_len(k))
  return(qSVs)
}