SaveCountsToH5: Save count_matrix.h5 files for SPRING integration

In SignacX: Cell Type Identification and Discovery from Single Cell Gene Expression Data

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")


## End(Not run)

SignacX documentation built on Nov. 18, 2021, 5:07 p.m.