Bulk RNAseq co-expression modules

Class for applying various co-expression module detection methods on top of bulk RNAseq data.

Usage

BulkCoExp(raw_data, meta_data, variable_info = NULL)

Arguments

raw_data

The raw count matrix. Rows = samples, columns = features.

meta_data

data.table Metadata information on the samples. Expects to have a sample_id column.

variable_info

data.table. Metadata information on the features. This is an optional table.

Value

Returns the BulkCoExp class for further operations.

Properties

raw_data

A numerical matrix of the provided raw data.

meta_data

A data.table with the meta-information about the samples.

variable_info

An optional data.table containing the variable info.

processed_data

A list in which various types of processed data will be stored.

outputs

A list in which key outputs will be stored.

params

A (nested) list that will store all the parameters of the applied function.

final_results

A data.table that will contain the final results.

Examples

# co-expression class over synthetic bulk counts (samples x genes)
syn <- synthetic_bulk_cor_matrix()
mat <- log1p(t(syn$counts))
meta <- data.table::data.table(sample_id = rownames(mat))
object <- BulkCoExp(raw_data = mat, meta_data = meta)
object
#> Bulk co-expression module class (BulkCoExp).
#>  Pre-processing done: FALSE.