Description Usage Arguments Value
Write a dgCMatrix to an h5 file similar to cellRanger format
1 2 | write_dgCMatrix_h5(mat, cols_are = "gene_names", h5_target,
ref_name = "mm10-1.2.0_premrna", gene_ids = NULL)
|
mat |
a dgCMatrix to write. |
cols_are |
Whether columns are "gene_names" or "sample_names". If "gene_names", mat will be transposed to match 10X conventions. |
h5_target |
The target .h5 file for output. |
ref_name |
Reference name for storing the data |
gene_ids |
If available, ENSEMBL IDs for each gene |
an .h5 file with these mappings from dgCMatrix -> .h5:
colnames(mat) -> /ref_name/barcodes (after transposition if cols_are == "gene_names")
rownames(mat) -> /ref_name/gene_names (after transposition if cols_are == "gene_names")
mat@x -> /ref_name/data
mat@i -> /ref_name/indices
mat@p -> /ref_name/indptr
gene_ids -> /ref_name/gene
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