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QC on the bulk dge data (DEPRECATED!)

preprocess_bulk_dge.Rd

This is a deprecated method and will raise an error. Please use qc_bulk_dge() and normalise_bulk_dge() instead.

Usage

preprocess_bulk_dge(
  object,
  group_col,
  norm_method = c("TMM", "TMMwsp", "RLE", "upperquartile", "none"),
  outlier_threshold = 2,
  min_prop = 0.2,
  .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.

norm_method

String. One of c("TMM", "TMMwsp", "RLE", "upperquartile", "none"). Please refer to edgeR::normLibSizes().

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.

.verbose

Boolean. Controls the verbosity of the function.

Value

Throws an error, as it is deprecated.