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Between Level Analysis

between_level.Rd

Performs a between-level analysis using LIMMA to compare specified levels within a condition.

Usage

between_level(
  data,
  rna_seq_data,
  meta,
  design,
  spline_params,
  condition,
  compared_levels,
  padjust_method,
  feature_names
)

Arguments

data

A matrix of data values.

rna_seq_data

An object containing the preprocessed RNA-seq data, such as the output from `limma::voom` or a similar preprocessing pipeline.

meta

A dataframe containing metadata, including a 'Time' column.

design

A design formula or matrix for the LIMMA analysis.

spline_params

A list of spline parameters for the analysis.

condition

A character string specifying the condition.

compared_levels

A vector of levels within the condition to compare.

padjust_method

A character string specifying the p-adjustment method.

feature_names

A non-empty character vector of feature names.

Value

A list containing top tables for the factor only and factor-time contrast.

See also

bs, ns, lmFit, eBayes, topTable, modify_limma_top_table