read10xH5 {CRMetrics}

Read 10x HDF5 files

Description

Read 10x HDF5 files

Usage

read10xH5(
  data.path,
  samples = NULL,
  type = c("raw", "filtered", "cellbender", "cellbender_filtered"),
  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

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)