deg_limma | R Documentation |
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.
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
)
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 |
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,
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