sce-utils.R

# Some common functions for manipulating bioconductor SingleCellExperiment objects

#' Return the corresponding ensembl gene id for a symbol in a given SCE
get_ensembl_id <- function(symbol, sce) {
  stopifnot(symbol %in% rowData(sce)$Symbol)
  rownames(sce)[rowData(sce)$Symbol == symbol]
}

#' Prepare an SCE read using read10XUtils for SC3
prepare_for_sc3 <- function(sce) {
  counts(sce) <- as.matrix(counts(sce))
  logcounts(sce) <- as.matrix(logcounts(sce))
  rowData(sce)$feature_symbol <- rowData(sce)$Symbol
  sce
}

#' Remove calculated rowData to cbind two or more SCEs together
remove_rowdata <- function(sce) {
  rowData(sce)[13:20] <- NULL
  sce
}