normalize_assay_data: Helper functions to normalize assay data into log2 space.

In facileverse/FacileData: A fluent API for accessing multi-assay high-throughput genomics data

Helper functions to normalize assay data into log2 space.

Description

This is defined for the assay_types defined within this package. If you are writing a package to handle new types of data, you need to define a normalize_assay_matrix.ASSAY_TYPE function. This is experimental.

Usage

normalize_assay_data(
  x,
  features,
  samples,
  batch = NULL,
  log = TRUE,
  prior.count = 0.1,
  main = NULL,
  verbose = FALSE,
  ...,
  .fds = NULL
)

Arguments

x	A matrix of raw/unnormalized assay data retrieved from within the fetch_assay_data() itself.
features	a feature descriptor data.frame that includes the feature_id's of the rows in x, as well as the assay name/type they were pulled from. We assert that all features come from the same assay type, and the rows here match 1:1 the rows in x.
samples	a sample descriptor for the columns in x. Rows here should match columns in x 1:1.
batch, main	parameters sent to remove_batch_effects() after assay data has been materialized.

facileverse/FacileData documentation built on April 12, 2025, 11:50 a.m.