This function read specific rows, associated with some genes, from a dense matrix stored in a HDF5 file.
Usage
read_gene_from_dense_h5(
gene_names,
matrix_h5_path,
index_genes = NULL,
check_intersect = TRUE,
add_rownames = FALSE
)Arguments
- gene_names
List of names of genes to be read.
- matrix_h5_path
Path to the HDF5 file where the expression matrix is stored. The file must contain the following fields:
genes: the names of the genes in the matrix.
cells: the names of the cells in the matrix.
expression_matrix: the expression matrix
- index_genes
Named vector where the names are the genes and the values the index of the row associated with a gene. If NULL, the function will calculate automatically this index. Defaults to NULL.
- check_intersect
Logical indicating if the function should check if all the provided genes are present in the matrix. Defaults to TRUE.
- add_rownames
Logical indicating if the function should add the cell names as column names for the extracted matrix. Defaults to FALSE.