write_dgCMatrix_h5: Write a dgCMatrix to an h5 file similar to cellRanger format

In AllenInstitute/scrattch.io: scrattch File Input/Output Handling

Description

Write a dgCMatrix to an h5 file similar to cellRanger format

Usage

write_dgCMatrix_h5(mat, cols_are = "gene_names", h5_target,
  ref_name = "mm10-1.2.0_premrna", gene_ids = NULL)

Arguments

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

Value

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

AllenInstitute/scrattch.io documentation built on Nov. 17, 2021, 10:06 a.m.