get10Xmatrix_h5

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

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)

Value

(list of) sparse expression matrix from 10X

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