sce: Helper functions for the processing of .loom and .h5ad files...

In Bioconductor/hcaquery: Conversion of single cell experiment output files to relational database

Description

convert a SummarizedExperiment assay to a sparse matrix representation

function to change SingleCellLoomExperiment object's assay matrix into sparse representation (dgCMatrix)

function to change SingleCellLoomExperiment object's assay matrix into sparse representation (dgRMatrix)

function to change SingleCellLoomExperiment object's assay matrix into sparse representation (DelayedMatrix)

function to change SingleCellLoomExperiment object's assay matrix into sparse representation (matrix)

convert a sparse matrix representation of the assay into a reformatted tibble

convert a dgCMatrix sparse matrix representation of the assay into a reformatted tibble

function to change SingleCellExperiment or SingleCellLoomExperiment object's rowData into a gene annotation table

function to change SingleCellExperiment or SingleCellLoomExperiment object's colData into a cell annotation table

Usage

loom_to_sce(loom_filepath)

h5ad_to_sce(h5ad_filepath)

to_sparse_matrix(matrix_obj)

.to_sparse_matrix.dgCMatrix(c_matrix)

.to_sparse_matrix.dgRMatrix(r_matrix)

.to_sparse_matrix.DelayedMatrix(d_matrix)

.to_sparse_matrix.matrix(m_matrix)

sparse_mtx_to_assay_tbl(sparse_matrix)

.sparse_matrix_to_assay_tbl.dgCMatrix(sparse_matrix)

sce_rowdata_to_gene_tbl(sce)

sce_coldata_to_cell_tbl(sce)

Arguments

loom_filepath	character() absolute path to downloaded .loom file
h5ad_filepath	character() absolute path to downloaded .h5ad file
sparse_matrix	dgCMatrix sparse matrix representation
sce	SingleCellExperiment or SingleCellLoomExperiment object
sce_obj	SummarizedExperiment (or subclass) object
dgCMatrix	sparse matrix
dgRMatrix	sparse matrix
DelayedMatrix	sparse matrix
matrix	sparse matrix

Value

SingleCellLoomExperiment object

SingleCellExperiment object

dgCMatrix sparse matrix representation

dgCMatrix sparse matrix representation

dgCMatrix sparse matrix representation

dgCMatrix sparse matrix representation

tibble with row_index, col_index, and value of each non-zero entry in the assay matrix

tibble of gene annotations

tibble of cell annotations

Bioconductor/hcaquery documentation built on Dec. 17, 2021, 10:56 a.m.