template_int_params.yml

---
# ==========================================================
# Integrative Report (RNA_Integrate.Rmd)
# ==========================================================

# --- Experiment identifiers ---
# Used in output filenames; avoid spaces/special characters.
mrna_experiment_id: "mrna_experiment_id_no_spaces"
small_rna_experiment_id: "smallrna_experiment_id_no_spaces"
integrative_experiment_id: "integrative_experiment_id_no_spaces"

# --- Tabulation software ---
# Choose how counts were generated/tabulated.
mrna_software_method: "counts_matrix | rsem | htseq | salmon | kallisto"
small_rna_software_method: "counts_matrix | tiny_rna"

# --- Input files ---
# Required only for mrna_software_method = counts_matrix.
# Leave blank for htseq, rsem, salmon, and kallisto.
mrna_counts_matrix: ""
# Required for small_rna_software_method = counts_matrix or tiny_rna.
small_rna_counts_matrix: "path/to/smallrna_counts_matrix.csv"

# Metadata must contain:
# counts_file, sample_name, condition, control
# counts_file is required only for htseq/rsem/salmon/kallisto mRNA runs.
# Leave counts_file blank for counts_matrix and tiny_rna.
mrna_metadata: "path/to/mrna_metadata.csv"
small_rna_metadata: "path/to/smallrna_metadata.csv"

# --- Gene table configuration ---
mrna_gene_table_method: "full_table | common_names_only | gene_class_only | no_table"
small_rna_gene_table_method: "full_table | common_names_only | gene_class_only | no_table"
# Integrative gene table must contain:
# sRNA_ID, sRNA_Name, sRNA_Class, Target_ID, Target_Name
gene_table: "path/to/integrative_gene_table.csv"

# --- DESeq2 output settings ---
generate_results_tables: TRUE
generate_pca: TRUE
generate_intra_condition: TRUE
generate_mean_reads: TRUE
save_mean_reads_interactive: FALSE
generate_ma: TRUE
generate_heatmap: TRUE

# --- Class-parameter files ---
small_rna_class_parameters: "path/to/smallrna_class_parameters.csv"
mrna_class_parameters: "path/to/mrna_class_parameters.csv"

# --- Significance and visualization settings ---
p_value_threshold: 0.05
fold_change_threshold: 1.3
lower_transparency: 0.2
upper_transparency: 0.9
customize_by_class: TRUE
customize_by_significance: FALSE

# --- Heatmap settings ---
heatmap_type: "complete | all_classes | selected_classes"
heatmap_selected_classes: ""

# --- Integrative output settings ---
generate_integrative_results_tables: TRUE
generate_cosmic_plots: TRUE
generate_slope_plots: TRUE
generate_statistical_analysis: TRUE

# --- Integrative comparison settings ---
# Must match comparison names generated from metadata conditions.
# Example: "mutant_vs_wt"
# Leave blank to use comparisons shared by both mRNA and small RNA runs.
cross_comparisons: ""

# --- Slope plot settings ---
# Leave blank to use all small RNA classes from the gene table.
# Example: "miRNA,ALG,CSR"
slope_plot_classes: ""

---