Repertoire Analysis of the Detected Clonotype
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Documentation for package ‘rTCRBCRr’ version 0.1.1
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| all_sample_all_chain_all_metrics_wide_format_dataframe | a dataframe of wide format |
| all_sample_all_chain_all_metrics_wide_format_dataframe_list | a dataframe list to combine rowwise. |
| all_sample_all_chain_individual_metrics_dataframe_list | a list of dataframes |
| all_sample_IGH_chain_all_metrics_wide_format_dataframe | a dataframe of wide format |
| all_sample_IGH_chain_all_metrics_wide_format_dataframe_list | a dataframe list to combine rowwise. |
| all_sample_IGH_chain_individual_metrics_dataframe_list | a list of dataframes |
| annotate_chain_name_and_isotype_name | Annotate chain name and isotype name |
| calculate_IGH_isotype_proportion | calculate_IGH_isotype_proportion |
| calculate_repertoire_metrics | calculate_repertoire_metrics |
| calibrate_proportion_by_clones | calibrate_proportion_by_clones |
| chain_separated_dataframe | a dataframe separated by chain name |
| combine_all_sample_repertoire_metrics | combine_all_sample_repertoire_metrics |
| compute_repertoire_metrics_by_chain_name | compute_repertoire_metrics_by_chain_name |
| convergent_clonotype_merged_dataframe | a dataframe where convergent clonotypes are merged |
| format_clonotype_to_immunarch_style | Convert clonotype dataframe to immunarch format |
| get_item_name_x_sample_name_for_each_metric | get_item_name_x_sample_name_for_each_metric |
| immunarch_style_dataframe | An converted dataframe to immunarch format |
| merge_convergent_clonotype | Merge convergent clonotype |
| nonproductive_CDR3aa_removed_dataframe | a dataframe with nonproductive CDR3aa removed |
| parse_mixcr | Parse mixcr format |
| parse_trust4 | Parse trust4 format |
| raw_input_clonotype_dataframe | Raw clonotype output from trust4 |
| remove_nonproductive_CDR3aa | Clean the clonotype dataframe |
| summarize_convergence_function | summarize_convergence_function |
| summarize_repertoire_metrics | summarize_repertoire_metrics |
| the global variables | Make variable names global to avoid CHECK notes |
| the_divergent_clonotype_dataframe_list | a list of dataframe where convergent clonotypes are merged |