get10Xmatrix_h5: get10Xmatrix_h5

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

get10Xmatrix_h5

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.