get10Xmatrix_h5#

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Last Updated: Mar 11, 2023

Description#

This function creates an expression matrix from a 10X h5 file path

Usage#

get10Xmatrix_h5(
  path_to_data,
  gene_ids = c("symbols", "ensembl"),
  remove_zero_rows = TRUE,
  split_by_type = TRUE
)

Arguments#

path_to_data

path to the 10X .h5 file

gene_ids

use gene symbols (default) or ensembl ids for the gene expression matrix

remove_zero_rows

removes rows with sum equal to zero

split_by_type

split into multiple matrices based on 3rd column of features.tsv(.gz)

Details#

If the .h5 10x file has multiple classes of features (e.g. expression vs QC probes) or modalities (e.g. RNA and protein), and split_by_type param is TRUE, multiple matrices will be returned

Value#

(list of) sparse expression matrix from 10X