Standalone function to read loom files from velocyto into R as CsparseMatrix, adapted from velocyto.R.

readLoomMatrices.R

#' Read loom files into R as CsparseMatrix, depending on Matrix and hdf5r
#' @param path to file loom file on disk
#' @param include.ambiguous logical, whether to also read the "ambiguous" counts from velocyto, default FALSE
#'
readLoomMatrices <- function(file, include.ambiguous=FALSE) {
  
  require(Matrix)
  require(hdf5r)
  
  engine='hdf5r'
  if (engine == 'hdf5r') {
    
    f <- hdf5r::H5File$new(file, mode='r')
    
    cells <- f[["col_attrs/CellID"]][]
    
    genes <- f[["row_attrs/Accession"]][]
    
    dl <- c(spliced="layers/spliced",
            unspliced="layers/unspliced",
            ambiguous="layers/ambiguous")
    
    if(!include.ambiguous) {
      dl <- dl[c("spliced", "unspliced")]
    }
    
    if("layers/spanning" %in% hdf5r::list.datasets(f)) {
      dl <- c(dl, c(spanning="layers/spanning"))
    }
    
    dlist <- lapply(dl, function(path) {
      m <- as(t(f[[path]][,]),'CsparseMatrix')
      rownames(m) <- genes; colnames(m) <- cells;
      return(m)
    })
    
    f$close_all()
    return(dlist)
    
  }
  
}