SignacX (version 2.2.5)

SaveCountsToH5: Save count_matrix.h5 files for SPRING integration

Description

To integrate with SPRING, SaveCountsToH5 saves expression matrices in a sparse ".h5" format to be read with SPRING notebooks in Jupyter.

Usage

SaveCountsToH5(D, data.dir, genome = "GRCh38")

Arguments

D

A list of count matrices

data.dir

directory (will be created if it does not exist) where results are saved

genome

default is GRCh38.

Value

matrix.h5 file, where each is background corrected

Examples

# NOT RUN {
# download single cell data for classification
file.dir = "https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_v3/"
file = "pbmc_1k_v3_filtered_feature_bc_matrix.h5"
download.file(paste0(file.dir, file), "Ex.h5")

# load data
library(Seurat)
E = Read10X_h5(filename = "Ex.h5")

# save counts to h5 files
SaveCountsToH5(E, data.dir = "counts_h5")

# }