read10xH5: Read 10x or cellbenders HDF5 files

In CRMetrics: Cell Ranger Output Filtering and Metrics Visualization

Read 10x or cellbenders HDF5 files

Description

Read 10x or cellbenders HDF5 files

Usage

read10xH5(
  data.path,
  samples = NULL,
  type = c("raw", "filtered", "cellbender", "cellbender_filtered"),
  technology = c("10x", "10xmultiome", "flex"),
  symbol = TRUE,
  sep = "!!",
  n.cores = 1,
  verbose = TRUE,
  unique.names = FALSE
)

Arguments

data.path	character
samples	character vector, select specific samples for processing (default = NULL)
type	name of H5 file to search for, "raw" and "filtered" are Cell Ranger count outputs, "cellbender" is output from CellBender after running script from saveCellbenderScript
technology	character Used single-cell technology (c("10x", "10xmultiome", "flex"))
symbol	logical Use gene SYMBOLs (TRUE) or ENSEMBL IDs (FALSE) (default = TRUE)
sep	character Separator for creating unique cell names from sample IDs and cell IDs (default = "!!")
n.cores	integer Number of cores (default = 1)
verbose	logical Print progress (default = TRUE)
unique.names	logical Create unique cell IDs (default = FALSE)

Value

list with sparse count matrices

Examples

## Not run: 
cms.h5 <- read10xH5(data.path = "/path/to/count/data")

## End(Not run)

CRMetrics documentation built on June 2, 2026, 9:08 a.m.