# Repertoire Analysis of the Detected Clonotype

## Documentation for package ‘rTCRBCRr’ version 0.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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