Generate a CDS from Bulk RNA-seq data

This function allows you to simulate single cell data from bulk RNA-seq data. It requires a TPM count matrix. The rationale is that TPM quantifies transcript counts per million reads, so you can think of this like 1 million UMI counts from a scRNA-seq experiment distributed in a certain way across the transcriptome. This function samples n_pseudocells with transcripts_per_pseudocell from this distribution. Then it creates a cell data set based on a matrix of these samples.

Importantly, this function cannot accurately identify transcriptional heterogenity within the bulk data. The sampling effect may reveal some potential heterogeneity but there is no method here for determining whether this is due to randomness or heterogeneity within the data.

The intended use of this function is to project a pseudocell cds onto an actual single cell data set. This can be used to help identify regions of UMAP space that are shared between the pseudocells and the real cells.

Note: The matrix rownames and row metadata for the returned cds will contain only the rownames from the input tpm_matrix. So these should share the same namespace as the single cell cds that the pseudocell data will be projected onto.

Usage

bb_pseudocells(
  tpm_matrix,
  n_pseudocells,
  transcripts_per_pseudocell,
  remove_genes = NULL
)

Arguments

tpm_matrix

A matrix of TPM counts from a bulk RNA experiment. A cds will be generated for each column in this matrix and the result combined.

n_pseudocells

The number of pseudocells to create. Should be length 1 or to specify a uniqe n_pseudocells for each dataset, a vector of the same length as the number of columns in tpm_matrix. This value will be recycled if necessary to match the number of columns in tpm_mtx.

transcripts_per_pseudocell

The number of transcripts to sample for each pseudocell. Should be similar to the median number of UMI in the single cell data the pseudocells will be projected onto. Should be length 1 or to specify a uniqe n_pseudocells for each dataset, a vector of the same length as the number of columns in tpm_matrix. This value will be recycled if necessary to match the number of columns in tpm_mtx.

remove_genes

A vector of genes to remove before sampling. Should be the same or similar to the genes removed from the single cell data the pseudocells will be projected onto, Default: NULL

Value

A cell data set

See also

map, reduce, map2, pmap tibble count, select components new_cell_data_set, combine_cds, preprocess_cds, reduce_dimension

Examples

if (FALSE) { # \dontrun{
if(interactive()){
 #EXAMPLE1
 }
} # }