# ##### MAIN SETTINGS ########
# settings that affect data processing
selected_reader: mqreader # which file reader should be used
selected_normalizer: None # which normalizer should be used
has_techrep: false # does the file have technical replicates (can be "true" or "false")
use_protein_id: false # should the protein id be used (can be "true" or "false"), or TODO
equal_variance: false # should equal variance be assumed for the t-test? (can be "true" or "false")
pathways: [] # list of pathways which should be analyzed
go_terms: [] # list of go_terms which should be analyzed
mqreader: {}
# ###### PLOT CREATION SETTINGS #######
# settings that determine which results will be created
plot_normalization_overview_all_normalizers_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_heatmap_overview_all_normalizers_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_detection_counts_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_detected_proteins_per_replicate_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_venn_results_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_venn_groups_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_pca_overview_settings:
create_plot: false
dfs_to_use: []
levels: []
no_missing_values: true # should missing values be neglected? (can be "true" or "false")
plot_intensity_histograms_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_relative_std_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_scatter_replicates_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_experiment_comparison_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_rank_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_pathway_analysis_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_go_analysis_settings:
create_plot: false
dfs_to_use: []
levels: []
plot_r_volcano_settings:
create_plot: false
dfs_to_use: []
levels: []
adj_pval: false # should the adjusted p-val be used? (can be "true" or "false")