SaveCountsToH5 {SignacX} | R Documentation |
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")
## End(Not run)
[Package SignacX version 2.2.5 Index]