Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.
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Convert single-cell data to GDS format, load it as a GDS-backed SingleCellExperiment, and perform memory-efficient downstream analysis.
library(SCArray)
library(SingleCellExperiment)
library(scuttle)
library(scater)
# Load example SingleCellExperiment
fn <- system.file("extdata", "example.rds", package="SCArray")
sce <- readRDS(fn)
# Convert to GDS file
scConvGDS(sce, "test.gds")
# Load SingleCellExperiment from GDS
sce_gds <- scExperiment("test.gds")
# Normalize counts
sce_gds <- logNormCounts(sce_gds)
# Row and column summarization
col_mean <- colMeans(assays(sce_gds)$counts)
mvar <- scRowMeanVar(assays(sce_gds)$counts)
# Memory-efficient PCA and UMAP
sce_gds <- scRunPCA(sce_gds)
sce_gds <- runUMAP(sce_gds)
# Plot PCA
plotReducedDim(sce_gds, dimred="PCA")
Input: A SingleCellExperiment object or matrix; Output: A GDS-backed SingleCellExperiment object with normalized counts and reduced dimensions.
SingleCellExperiment objects) to GDS format using scConvGDS.SingleCellExperiment using scExperiment.colMeans, rowMeans, scRowMeanVar) on GDS-backed DelayedMatrix objects.scRunPCA.SingleCellExperiment object or a dense/sparse matrix (e.g., dgCMatrix)..gds) containing compressed assay data.TRUE/FALSE): Global option to enable displaying debug information during SCArray operations.plotReducedDim (e.g., "PCA", "UMAP").scRunPCA instead of scater::runPCA for large-scale datasets to avoid high memory usage from realizing the full matrix in memory.options(SCArray.verbose=TRUE) to track GDS-backed matrix operations.scClose if manually opened with scOpen.scater::runPCA) on very large GDS-backed objects, which triggers in-memory realization and defeats the out-of-memory benefit. Use scRunPCA instead.DelayedMatrix objects, meaning operations are delayed until explicitly realized.HDF5Array: For HDF5-backed out-of-memory data storage and manipulation.TileDBArray: For TileDB-backed multi-dimensional array storage.LoomExperiment: For Loom-backed single-cell data storage.还没有评价。欢迎分享你的使用感受。
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