Bulk RNAseq differential gene expression class

Class for coordinating differential gene expression analyses with subsequent GSE in a structured format. Additionally, the class will store the counts in edgeR::DGEList() for subsequent processing.

Usage

BulkDge(
  raw_counts,
  meta_data,
  variable_info = NULL,
  alternative_gene_id = NULL
)

Arguments

raw_counts: matrix. The raw count matrix. Rows = genes, columns = samples. Note: this is different from the BulkCoExp() class!
meta_data: data.table. Metadata information on the samples. It expects to have a column sample_id and case_control column.
variable_info: data.table. Metadata information on the features. This is an optional table. Defaults to NULL.
alternative_gene_id: String. Optional alternative gene identifier to be used. Must be a column of variable_info!

Value

Returns the BulkDge class for further operations.

Properties

raw_counts: 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.
outputs: A list in which key outputs will be stored.
plots: A list with the plots that are generated during subsequent QC steps.
params: A (nested) list that will store all the parameters of the applied function.
final_results: A list in which final results will be stored.