deg_limma: Differential expression using limma package

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Differential expression using limma package

Description

Used in the limma_value function to perform DEG analysis using the limma package. It is not recommended to use this function on its own.

Usage

deg_limma(
  processed_data,
  max_p_limma = 0.1,
  min_fc_limma = 2,
  raw_counts,
  counts_deg_method,
  prior_counts,
  data_file_format,
  selected_comparisons = NULL,
  sample_info = NULL,
  model_factors = NULL,
  block_factor = NULL
)

Arguments

processed_data	Data that has been through the pre-processing
max_p_limma	Significant p-value to use for the fold-change values
min_fc_limma	Minimum fold-change to include in the results
raw_counts	The matrix of counts before processing for gene expression data
counts_deg_method	The method or package being used for the DEG analysis
prior_counts	The constant added to the log transformation from pre-processing
data_file_format	Type of gene data being examined
selected_comparisons	Selected comparisons to analyze in the DEG analysis
sample_info	Experiment file information for grouping
model_factors	Vector of selected factors and interaction terms from the model design
block_factor	The selected factors for batch effect

Value

The return value is the results of the DEG analysis. These results are filtered and formatted by the limma_value function. processed_data = processed_data,

espors/idepGolem documentation built on Oct. 27, 2024, 4:56 a.m.