loom_to_se: Convert: 'loom' ==> 'SummarizedExperiment'

In bschilder/scKirby: Automated ingestion and conversion of various single-cell data formats.

Convert: loom ==> SummarizedExperiment

Description

Convert: loom ==> SummarizedExperiment

Usage

loom_to_se(obj, as_sce = FALSE, verbose = TRUE, ...)

Arguments

obj	A single-cell object supported by scKirby. See converters for a table of all supported conversions.
as_sce	Convert to a SingleCellExperiment format.
verbose	Print messages.
...	Arguments passed on to SeuratDisk::LoadLoom assay Name of assay to store expression data as; if NULL, will search for an HDF5 attribute named SEURAT_ASSAY or an attribute dataset named /attrs/SEURAT_ASSAY for assay name. If not found, defaults to “RNA” cells Name of dataset in /col_attrs with cell names features Name of dataset in /row_attrs with feature names normalized Name of matrix in /layers to store normalized data as; pass “/matrix” to store /matrix as normalized data instead of raw counts scaled Name of dataset in /layers to store scaled data as filter Keep only selected cells and/or features as specified by /col_attrs/Valid and /row_attrs/Valid, respectively

Examples

library(Seurat)
obj <- example_obj("loom")
obj2 <- loom_to_se(obj)

bschilder/scKirby documentation built on Oct. 2, 2024, 10:16 p.m.