SignacX: SaveCountsToH5 – R documentation

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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")


## End(Not run)

SignacX

Cell Type Identification and Discovery from Single Cell Gene Expression Data

v2.2.0

GPL-3

Authors

Mathew Chamberlain [aut, cre], Virginia Savova [aut], Richa Hanamsagar [aut], Frank Nestle [aut], Emanuele de Rinaldis [aut], Sanofi US [fnd]

Initial release

2021-02-24