R/TENxMatrixSeed-class.R

In Bioconductor/HDF5Array: HDF5 datasets as array-like objects in R

### =========================================================================
### TENxMatrixSeed objects
### -------------------------------------------------------------------------


setClass("TENxMatrixSeed", contains="CSC_H5SparseMatrixSeed")


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### Low-level helpers
###

.find_rownames_dataset <- function(filepath, group)
{
    name <- "genes"
    if (h5exists(filepath, paste(group, name, sep="/")))
        return(name)
    name <- "features/id"
    if (h5exists(filepath, paste(group, name, sep="/")))
        return(name)
    NULL
}

### Return the rownames of the matrix.
.load_tenx_rownames <- function(filepath, group)
{
    name <- .find_rownames_dataset(filepath, group)
    if (is.null(name))
        return(NULL)
    read_h5sparse_component(filepath, group, name)
}

### Return the colnames of the matrix.
.load_tenx_barcodes <- function(filepath, group)
{
    if (!h5exists(filepath, paste0(group, "/barcodes")))
        return(NULL)
    read_h5sparse_component(filepath, group, "barcodes")
}


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### Constructor
###

TENxMatrixSeed <- function(filepath, group="matrix")
{
    seed0 <- H5SparseMatrixSeed(filepath, group)

    ## dimnames
    rownames <- .load_tenx_rownames(seed0@filepath, seed0@group)
    stopifnot(is.null(rownames) || length(rownames) == seed0@dim[[1L]])
    colnames <- .load_tenx_barcodes(seed0@filepath, seed0@group)
    stopifnot(is.null(colnames) || length(colnames) == seed0@dim[[2L]])
    dimnames <- list(rownames, colnames)

    new2("TENxMatrixSeed", seed0, dimnames=dimnames)
}