| Title: | Simulate Bulk RNA-seq Datasets from Single-Cell Datasets |
|---|---|
| Description: | SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations. |
| Authors: | Alexander Dietrich [aut, cre] |
| Maintainer: | Alexander Dietrich <[email protected]> |
| License: | GPL-3 + file LICENSE |
| Version: | 1.9.0 |
| Built: | 2024-11-30 05:21:43 UTC |
| Source: | https://github.com/bioc/SimBu |
needs a sparse matrix with cells in columns and genes in rows. You can find the detailed explaination here: http://cole-trapnell-lab.github.io/monocle-release/docs/#census
census( matrix, exp_capture_rate = 0.25, expr_threshold = 0, BPPARAM = BiocParallel::bpparam(), run_parallel = FALSE )census( matrix, exp_capture_rate = 0.25, expr_threshold = 0, BPPARAM = BiocParallel::bpparam(), run_parallel = FALSE )
matrix |
sparse count matrix; cells in columns, genes in rows |
exp_capture_rate |
expected capture rate; default=0.25 |
expr_threshold |
expression threshold; default=0 |
BPPARAM |
BiocParallel::bpparam() by default; if specific number of threads x want to be used, insert: BiocParallel::MulticoreParam(workers = x) |
run_parallel |
boolean, decide if multi-threaded calculation will be run. FALSE by default |
a vector for each cell-type, with a scaling factor which can be used to transform the counts of the matrix
tpm <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) cen <- SimBu::census(tpm)tpm <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) cen <- SimBu::census(tpm)
Build SummarizedExperiment using local annotation and count matrix R objects
dataset( annotation, count_matrix = NULL, tpm_matrix = NULL, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )dataset( annotation, count_matrix = NULL, tpm_matrix = NULL, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )
annotation |
(mandatory) dataframe; needs columns 'ID' and 'cell_type'; 'ID' needs to be equal with cell_names in count_matrix |
count_matrix |
(mandatory) sparse count matrix; raw count data is expected with genes in rows, cells in columns |
tpm_matrix |
sparse count matrix; TPM like count data is expected with genes in rows, cells in columns |
name |
name of the dataset; will be used for new unique IDs of cells |
spike_in_col |
which column in annotation contains information on spike_in counts, which can be used to re-scale counts; mandatory for spike_in scaling factor in simulation |
additional_cols |
list of column names in annotation, that should be stored as well in dataset object |
filter_genes |
boolean, if TRUE, removes all genes with 0 expression over all samples & genes with variance below |
variance_cutoff |
numeric, is only applied if |
type_abundance_cutoff |
numeric, remove all cells, whose cell-type appears less then the given value. This removes low abundant cell-types |
scale_tpm |
boolean, if TRUE (default) the cells in tpm_matrix will be scaled to sum up to 1e6 |
Return a SummarizedExperiment object
counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c(rep("T cells CD4", 300)) ) ds <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset")counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c(rep("T cells CD4", 300)) ) ds <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset")
Build SummarizedExperiment using a h5ad file for the counts
dataset_h5ad( h5ad_file_counts, h5ad_file_tpm = NULL, cell_id_col = "ID", cell_type_col = "cell_type", cells_in_obs = TRUE, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )dataset_h5ad( h5ad_file_counts, h5ad_file_tpm = NULL, cell_id_col = "ID", cell_type_col = "cell_type", cells_in_obs = TRUE, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )
h5ad_file_counts |
(mandatory) h5ad file with raw count data |
h5ad_file_tpm |
h5ad file with TPM count data |
cell_id_col |
(mandatory) name of column in Seurat meta.data with unique cell ids; 0 for rownames |
cell_type_col |
(mandatory) name of column in Seurat meta.data with cell type name |
cells_in_obs |
boolean, if TRUE, cell identifiers are taken from |
name |
name of the dataset; will be used for new unique IDs of cells#' @param spike_in_col which column in annotation contains information on spike_in counts, which can be used to re-scale counts; mandatory for spike_in scaling factor in simulation |
spike_in_col |
which column in annotation contains information on spike_in counts, which can be used to re-scale counts; mandatory for spike_in scaling factor in simulation |
additional_cols |
list of column names in annotation, that should be stored as well in dataset object |
filter_genes |
boolean, if TRUE, removes all genes with 0 expression over all samples & genes with variance below |
variance_cutoff |
numeric, is only applied if |
type_abundance_cutoff |
numeric, remove all cells, whose cell-type appears less then the given value. This removes low abundant cell-types |
scale_tpm |
boolean, if TRUE (default) the cells in tpm_matrix will be scaled to sum up to 1e6 |
Return a SummarizedExperiment object
# h5 <- system.file("extdata", "anndata.h5ad", package = "SimBu") # ds_h5ad <- SimBu::dataset_h5ad( # h5ad_file_counts = h5, # name = "h5ad_dataset", # cell_id_col = "id", # this will use the 'id' column of the metadata as cell identifiers # cell_type_col = "group", # this will use the 'group' column of the metadata as cell type info # cells_in_obs = TRUE # ) # in case your cell information is stored in the var layer, switch to FALSE# h5 <- system.file("extdata", "anndata.h5ad", package = "SimBu") # ds_h5ad <- SimBu::dataset_h5ad( # h5ad_file_counts = h5, # name = "h5ad_dataset", # cell_id_col = "id", # this will use the 'id' column of the metadata as cell identifiers # cell_type_col = "group", # this will use the 'group' column of the metadata as cell type info # cells_in_obs = TRUE # ) # in case your cell information is stored in the var layer, switch to FALSE
The objects need to have the same number of assays in order to work.
dataset_merge( dataset_list, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )dataset_merge( dataset_list, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )
dataset_list |
(mandatory) list of SummarizedExperiment objects |
name |
name of the new dataset |
spike_in_col |
which column in annotation contains information on spike_in counts, which can be used to re-scale counts; mandatory for spike_in scaling factor in simulation |
additional_cols |
list of column names in annotation, that should be stored as well in dataset object |
filter_genes |
boolean, if TRUE, removes all genes with 0 expression over all samples & genes with variance below |
variance_cutoff |
numeric, is only applied if |
type_abundance_cutoff |
numeric, remove all cells, whose cell-type appears less then the given value. This removes low abundant cell-types |
scale_tpm |
boolean, if TRUE (default) the cells in tpm_matrix will be scaled to sum up to 1e6 |
SummarizedExperiment object
counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c(rep("T cells CD4", 300)) ) ds1 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset1") ds2 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset2") ds_merged <- SimBu::dataset_merge(list(ds1, ds2))counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c(rep("T cells CD4", 300)) ) ds1 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset1") ds2 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset2") ds_merged <- SimBu::dataset_merge(list(ds1, ds2))
Build SummarizedExperiment using a Seurat object
dataset_seurat( seurat_obj, counts_layer, cell_id_col, cell_type_col, assay = NULL, tpm_layer = NULL, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )dataset_seurat( seurat_obj, counts_layer, cell_id_col, cell_type_col, assay = NULL, tpm_layer = NULL, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )
seurat_obj |
(mandatory) Seurat object with TPM counts |
counts_layer |
(mandatory) name of assay in Seurat object which contains count data in 'counts' slot |
cell_id_col |
(mandatory) name of column in Seurat meta.data with unique cell ids |
cell_type_col |
(mandatory) name of column in Seurat meta.data with cell type name |
assay |
name of the Seurat objecy assay that should be used. If NULL (default), the currently active assay is used |
tpm_layer |
name of assay in Seurat object which contains TPM data in 'counts' slot |
name |
name of the dataset; will be used for new unique IDs of cells |
spike_in_col |
which column in annotation contains information on spike_in counts, which can be used to re-scale counts; mandatory for spike_in scaling factor in simulation |
additional_cols |
list of column names in annotation, that should be stored as well in dataset object |
filter_genes |
boolean, if TRUE, removes all genes with 0 expression over all samples & genes with variance below |
variance_cutoff |
numeric, is only applied if |
type_abundance_cutoff |
numeric, remove all cells, whose cell-type appears less then the given value. This removes low abundant cell-types |
scale_tpm |
boolean, if TRUE (default) the cells in tpm_matrix will be scaled to sum up to 1e6 |
Return a SummarizedExperiment object
counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell-", rep(1:300)) colnames(tpm) <- paste0("cell-", rep(1:300)) rownames(counts) <- paste0("gene-", rep(1:1000)) rownames(tpm) <- paste0("gene-", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell-", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ), row.names = paste0("cell-", rep(1:300)) ) seurat_obj <- Seurat::CreateSeuratObject(counts = counts, assay = "gene_expression", meta.data = annotation) SeuratObject::LayerData(seurat_obj, assay = "gene_expression", layer = "data") <- tpm ds_seurat <- SimBu::dataset_seurat( seurat_obj = seurat_obj, counts_layer = "counts", cell_id_col = "ID", cell_type_col = "cell_type", tpm_layer = "data", name = "seurat_dataset" )counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell-", rep(1:300)) colnames(tpm) <- paste0("cell-", rep(1:300)) rownames(counts) <- paste0("gene-", rep(1:1000)) rownames(tpm) <- paste0("gene-", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell-", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ), row.names = paste0("cell-", rep(1:300)) ) seurat_obj <- Seurat::CreateSeuratObject(counts = counts, assay = "gene_expression", meta.data = annotation) SeuratObject::LayerData(seurat_obj, assay = "gene_expression", layer = "data") <- tpm ds_seurat <- SimBu::dataset_seurat( seurat_obj = seurat_obj, counts_layer = "counts", cell_id_col = "ID", cell_type_col = "cell_type", tpm_layer = "data", name = "seurat_dataset" )
Build SummarizedExperiment using a single sfaira entry ID
dataset_sfaira( sfaira_id, sfaira_setup, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, force = FALSE, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )dataset_sfaira( sfaira_id, sfaira_setup, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, force = FALSE, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )
sfaira_id |
(mandatory) ID of a sfaira dataset |
sfaira_setup |
(mandatory) the sfaira setup; given by |
name |
name of the dataset; will be used for new unique IDs of cells |
spike_in_col |
which column in annotation contains information on spike_in counts, which can be used to re-scale counts |
additional_cols |
list of column names in annotation, that should be stored as well in dataset object |
force |
boolean, if TRUE, datasets without annotation will be downloaded, FALSE otherwise (default) |
filter_genes |
boolean, if TRUE, removes all genes with 0 expression over all samples & genes with variance below |
variance_cutoff |
numeric, is only applied if |
type_abundance_cutoff |
numeric, remove all cells, whose cell-type appears less then the given value. This removes low abundant cell-types |
scale_tpm |
boolean, if TRUE (default) the cells in tpm_matrix will be scaled to sum up to 1e6 |
dataset object
setup_list <- SimBu::setup_sfaira(tempdir()) ds <- SimBu::dataset_sfaira( sfaira_id = "homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x", sfaira_setup = setup_list, name = "test_dataset" )setup_list <- SimBu::setup_sfaira(tempdir()) ds <- SimBu::dataset_sfaira( sfaira_id = "homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x", sfaira_setup = setup_list, name = "test_dataset" )
You can apply different filters on the whole data-zoo of sfaria; the resulting single-cell datasets will be combined into a single dataset which you can use for simulation Note: only datasets in sfaira with annotation are considered!
dataset_sfaira_multiple( organisms = NULL, tissues = NULL, assays = NULL, sfaira_setup, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )dataset_sfaira_multiple( organisms = NULL, tissues = NULL, assays = NULL, sfaira_setup, name = "SimBu_dataset", spike_in_col = NULL, additional_cols = NULL, filter_genes = TRUE, variance_cutoff = 0, type_abundance_cutoff = 0, scale_tpm = TRUE )
organisms |
(mandatory) list of organisms (only human and mouse available) |
tissues |
(mandatory) list of tissues |
assays |
(mandatory) list of assays |
sfaira_setup |
(mandatory) the sfaira setup; given by |
name |
name of the dataset; will be used for new unique IDs of cells |
spike_in_col |
which column in annotation contains information on spike_in counts, which can be used to re-scale counts |
additional_cols |
list of column names in annotation, that should be stored as well in dataset object |
filter_genes |
boolean, if TRUE, removes all genes with 0 expression over all samples & genes with variance below |
variance_cutoff |
numeric, is only applied if |
type_abundance_cutoff |
numeric, remove all cells, whose cell-type appears less then the given value. This removes low abundant cell-types |
scale_tpm |
boolean, if TRUE (default) the cells in tpm_matrix will be scaled to sum up to 1e6 |
dataset object
setup_list <- SimBu::setup_sfaira(tempdir()) ds_human_lung <- SimBu::dataset_sfaira_multiple( sfaira_setup = setup_list, organisms = "Homo sapiens", tissues = "lung parenchyma", assay = "10x 3' v2", name = "human_lung" )setup_list <- SimBu::setup_sfaira(tempdir()) ds_human_lung <- SimBu::dataset_sfaira_multiple( sfaira_setup = setup_list, organisms = "Homo sapiens", tissues = "lung parenchyma", assay = "10x 3' v2", name = "human_lung" )
we recommend to only merge simulations from the same dataset object, otherwise the count matrices might not correspond on the gene level
merge_simulations(simulation_list)merge_simulations(simulation_list)
simulation_list |
a list of simulations |
named list; bulk a SummarizedExperiment object, where the assays store the simulated bulk RNAseq datasets. Can hold either one or two assays, depending on how many matrices were present in the dataset
cell-fractions is a dataframe with the simulated cell-fractions per sample;
scaling_vector scaling value for each cell in dataset
counts <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ) ) dataset <- SimBu::dataset( annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset" ) s1 <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) s2 <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) s <- SimBu::merge_simulations(list(s1, s2))counts <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ) ) dataset <- SimBu::dataset( annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset" ) s1 <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) s2 <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) s <- SimBu::merge_simulations(list(s1, s2))
Plot the cell-type fractions in your simulated dataset
plot_simulation(simulation)plot_simulation(simulation)
simulation |
a simulation object generated by |
a gpplot2 barplot
counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ) ) dataset <- SimBu::dataset( annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset" ) s <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) SimBu::plot_simulation(s)counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ) ) dataset <- SimBu::dataset( annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset" ) s <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) SimBu::plot_simulation(s)
Save the expression matrix of a simulated pseudo-bulk dataset to a file
save_simulation(simulation, filename, assay = "bulk_counts")save_simulation(simulation, filename, assay = "bulk_counts")
simulation |
the result of simulate_bulk() |
filename |
the filename where to save the expression matrix to |
assay |
name of the assay in simulation to save, default to bulk_counts |
write a file
counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ) ) dataset <- SimBu::dataset( annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset" ) s <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) save_simulation(s, tempfile())counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ) ) dataset <- SimBu::dataset( annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset" ) s <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) save_simulation(s, tempfile())
If you want to download datasets from Sfaira, you need to specify a directory where the datasets are saved into. Additionally, when this function is called for the first time, a conda environment will be established and sfaira along all of its dependencies are installed. This can take some time but will be only performed one single time, as the environment can be re-used.
setup_sfaira(basedir)setup_sfaira(basedir)
basedir |
name of the directory, where the raw files will be downloaded into |
list with sfaira file directories; must be used as input for other sfaira based functions
setup_list <- setup_sfaira(basedir = tempdir())setup_list <- setup_sfaira(basedir = tempdir())
Gives an overview of the possible datasets you can use from the sfaira database
sfaira_overview(setup_list)sfaira_overview(setup_list)
setup_list |
the sfaira setup; given by |
a dataframe with information on each dataset
setup_list <- setup_sfaira(basedir = tempdir()) # all_datasets <- sfaira_overview(setup_list)setup_list <- setup_sfaira(basedir = tempdir()) # all_datasets <- sfaira_overview(setup_list)
As complex tissues are typically composed of various cell types, deconvolution tools have been developed to computationally infer their cellular composition from bulk RNA sequencing (RNA-seq) data. To comprehensively assess deconvolution performance, gold-standard datasets are indispensable. The simulation of ‘pseudo-bulk’ data, generated by aggregating single-cell RNA-seq (scRNA-seq) expression profiles in pre-defined proportions, offers a scalable and cost-effective way of generating these gold-standard datasets. SimBu was developed to simulate pseudo-bulk samples based on various simulation scenarios, designed to test specific features of deconvolution methods. A unique feature of SimBu is the modelling of cell-type-specific mRNA bias using experimentally-derived or data-driven scaling factors.
You will need an annotated scRNA-seq dataset (as matrix file, h5ad file, Seurat object), which is the baseline for the simulations. Use the dataset_* functions to generate a SummarizedExperiment, that holds all important information. It is also possible to access scRNA-seq datasets through the public database Sfaira, by using the functions dataset_sfaira() and dataset_sfaira_multiple().
Use the simulate_bulk() function to generate multiple pseudo-bulk samples, which will be returned as a SummarizedExperiment. You can adapt the cell type fractions in each sample by changing the scenario parameter.
Inspect the cell type composition of your simulations with the plot_simulation() function.
This function allows you to create a full pseudo-bulk RNAseq dataset. You need to provide a SummarizedExperiment from which the cells
will be sampled for the simulation. Also a scenario has to be selected, where you can choose how the cells will be sampled and a
scaling_factor on how the read counts will be transformed proir to the simulation.
simulate_bulk( data, scenario = c("even", "random", "mirror_db", "weighted", "pure", "custom"), scaling_factor = c("NONE", "census", "spike_in", "custom", "read_number", "expressed_genes", "annotation_column", "epic", "abis", "quantiseq"), scaling_factor_single_cell = TRUE, weighted_cell_type = NULL, weighted_amount = NULL, pure_cell_type = NULL, custom_scenario_data = NULL, custom_scaling_vector = NULL, balance_even_mirror_scenario = 0.01, remove_bias_in_counts = FALSE, remove_bias_in_counts_method = "read-number", norm_counts = FALSE, nsamples = 100, ncells = 1000, total_read_counts = NULL, whitelist = NULL, blacklist = NULL, seed = NA, BPPARAM = BiocParallel::bpparam(), run_parallel = FALSE )simulate_bulk( data, scenario = c("even", "random", "mirror_db", "weighted", "pure", "custom"), scaling_factor = c("NONE", "census", "spike_in", "custom", "read_number", "expressed_genes", "annotation_column", "epic", "abis", "quantiseq"), scaling_factor_single_cell = TRUE, weighted_cell_type = NULL, weighted_amount = NULL, pure_cell_type = NULL, custom_scenario_data = NULL, custom_scaling_vector = NULL, balance_even_mirror_scenario = 0.01, remove_bias_in_counts = FALSE, remove_bias_in_counts_method = "read-number", norm_counts = FALSE, nsamples = 100, ncells = 1000, total_read_counts = NULL, whitelist = NULL, blacklist = NULL, seed = NA, BPPARAM = BiocParallel::bpparam(), run_parallel = FALSE )
data |
(mandatory) SummarizedExperiment object |
scenario |
(mandatory) select on of the pre-defined cell-type fraction scenarios; possible are: |
scaling_factor |
(mandatory) name of scaling factor; possible are: |
scaling_factor_single_cell |
boolean: decide if a scaling value for each single cell is calculated (default) or the median of all scaling values for each cell type is calculated |
weighted_cell_type |
name of cell-type used for |
weighted_amount |
fraction of cell-type used for |
pure_cell_type |
name of cell-type for |
custom_scenario_data |
dataframe; needs to be of size |
custom_scaling_vector |
named vector with custom scaling values for cell-types. Cell-types that do not occur in this vector but are present in the dataset will be set to 1; mandatory for |
balance_even_mirror_scenario |
balancing value for the |
remove_bias_in_counts |
boolean; if TRUE the internal mRNA bias that is present in count data will be removed using the number of reads mapped to each cell. Default to FALSE |
remove_bias_in_counts_method |
'read-number' (default) or 'gene-number'; method with which the mRNA bias in counts will be removed |
norm_counts |
boolean; if TRUE the samples simulated with counts will be normalized to CPMs, default is FALSE |
nsamples |
numeric; number of samples in pseudo-bulk RNAseq dataset (default = 100) |
ncells |
numeric; number of cells in each dataset (default = 1000) |
total_read_counts |
numeric; sets the total read count value for each sample |
whitelist |
list; give a list of cell-types you want to keep for the simulation; if NULL, all are used |
blacklist |
list; give a list of cell-types you want to remove for the simulation; if NULL, all are used; is applied after whitelist |
seed |
numeric; specifiy a seed for RNG. This effects cell sampling; with a fixed seed you will always sample the same cells for each sample (seed value is incrased by 1 for each sample). Default = NA (two simulation runs will sample different cells). |
BPPARAM |
BiocParallel::bpparam() by default; if specific number of threads x want to be used, insert: BiocParallel::MulticoreParam(workers = x) |
run_parallel |
boolean, decide if multi-threaded calculation will be run. FALSE by default |
named list; bulk a SummarizedExperiment object, where the assays store the simulated bulk RNAseq datasets. Can hold either one or two assays, depending on how many matrices were present in the dataset
cell-fractions is a dataframe with the simulated cell-fractions per sample;
scaling_vector scaling value for each cell in dataset
# generate sample single-cell data to work with: counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ) ) dataset <- SimBu::dataset( annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset" ) # this creates a basic pseudo-bulk dataset with uniform cell-type distribution # and no additional transformation of the data with 10 samples and 2000 cells each s <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) # use a blacklist to exclude certain cell-types for the simulation s <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 2000, blacklist = c("Monocytes", "Macrophages") ) # use the pure scenario to only have B cells s <- SimBu::simulate_bulk(dataset, scenario = "pure", scaling_factor = "NONE", nsamples = 10, ncells = 100, pure_cell_type = "B cells" ) # simulate a dataset with custom cell-type fraction for each of the 3 samples fractions <- data.frame( "B cells" = c(0.2, 0.4, 0.2), "T cells CD4" = c(0.4, 0.2, 0.1), "Macrophages" = c(0.4, 0.4, 0.7), check.names = FALSE ) s <- SimBu::simulate_bulk(dataset, scenario = "custom", scaling_factor = "NONE", nsamples = 3, ncells = 2000, custom_scenario_data = fractions )# generate sample single-cell data to work with: counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm)) colnames(counts) <- paste0("cell_", rep(1:300)) colnames(tpm) <- paste0("cell_", rep(1:300)) rownames(counts) <- paste0("gene_", rep(1:1000)) rownames(tpm) <- paste0("gene_", rep(1:1000)) annotation <- data.frame( "ID" = paste0("cell_", rep(1:300)), "cell_type" = c( rep("T cells CD4", 50), rep("T cells CD8", 50), rep("Macrophages", 100), rep("NK cells", 10), rep("B cells", 70), rep("Monocytes", 20) ) ) dataset <- SimBu::dataset( annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset" ) # this creates a basic pseudo-bulk dataset with uniform cell-type distribution # and no additional transformation of the data with 10 samples and 2000 cells each s <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 100 ) # use a blacklist to exclude certain cell-types for the simulation s <- SimBu::simulate_bulk(dataset, scenario = "even", scaling_factor = "NONE", nsamples = 10, ncells = 2000, blacklist = c("Monocytes", "Macrophages") ) # use the pure scenario to only have B cells s <- SimBu::simulate_bulk(dataset, scenario = "pure", scaling_factor = "NONE", nsamples = 10, ncells = 100, pure_cell_type = "B cells" ) # simulate a dataset with custom cell-type fraction for each of the 3 samples fractions <- data.frame( "B cells" = c(0.2, 0.4, 0.2), "T cells CD4" = c(0.4, 0.2, 0.1), "Macrophages" = c(0.4, 0.4, 0.7), check.names = FALSE ) s <- SimBu::simulate_bulk(dataset, scenario = "custom", scaling_factor = "NONE", nsamples = 3, ncells = 2000, custom_scenario_data = fractions )