QC on the bulk dge data

This function will do QC on the bulk data and remove outlier samples that show substantially lower expression of genes compared to the rest of the data and remove lowly expressed genes.

Usage

qc_bulk_dge(
  object,
  group_col,
  outlier_threshold = 2,
  min_prop = 0.2,
  min_count = 10,
  .verbose = TRUE
)

Arguments

object

The underlying class, see BulkDge().

group_col

String. The column in the metadata that will contain the contrast groups. Needs to be part of the metadata stored in the class.

outlier_threshold

Float. Number of standard deviations in terms of percentage genes detected you allow before removing a sample. Defaults to 2.

min_prop

Float. Minimum proportion of samples in which the gene has to be identified in.

min_count

Float. Minimum number of counts (cpm) to be detected in min_prop of the samples (in cohorts defined by groups_coll)

.verbose

Boolean. Controls the verbosity of the function.

Value

Returns the class with the processed_data data slot populated and applied parameters added to the params slot.