Installation | Example code | Attach packages | Read raw data files (trust generated for example) into a list of data frames | Tidy up the clonotype dataframes | Calculate and merge repertoire metrics by chains for each sample in the list | Calculate and merge repertoire metrics by IGH isotypes for each sample in the list | Clonotype repertoire metrics formulas | Acknowledgements
Package: rTCRBCRr 0.1.1
Lizhong Ding
rTCRBCRr: Repertoire Analysis of the Detected Clonotype
The 'TRUST4' or 'MiXCR' is used to identify the clonotypes. The goal of 'rTCRBCRr' is to process the results from these clonotyping tools, and analyze the clonotype repertoire metrics based on chain names and IGH isotypes. The manuscript is still under preparation for publication for now. The references describing the methods in this package will be added later.
Authors:
rTCRBCRr_0.1.1.tar.gz
rTCRBCRr_0.1.1.tar.gz(r-4.7-any)rTCRBCRr_0.1.1.tar.gz(r-4.6-any)
rTCRBCRr_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rTCRBCRr/json (API)
| # Install 'rTCRBCRr' in R: |
| install.packages('rTCRBCRr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- 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
- chain_separated_dataframe - A dataframe separated by chain name
- convergent_clonotype_merged_dataframe - A dataframe where convergent clonotypes are merged
- immunarch_style_dataframe - An converted dataframe to immunarch format
- nonproductive_CDR3aa_removed_dataframe - A dataframe with nonproductive CDR3aa removed
- raw_input_clonotype_dataframe - Raw clonotype output from trust4
- the_divergent_clonotype_dataframe_list - A list of dataframe where convergent clonotypes are merged
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:b9e2f989e9. Checks:2 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 131 | ||
| source / vignettes | OK | 226 | ||
| linux-release-x86_64 | NOTE | 135 | ||
| wasm-release | OK | 110 |
Exports:annotate_chain_name_and_isotype_namecalculate_IGH_isotype_proportioncalculate_repertoire_metricscalibrate_proportion_by_clonescombine_all_sample_repertoire_metricscompute_repertoire_metrics_by_chain_nameformat_clonotype_to_immunarch_styleget_item_name_x_sample_name_for_each_metricmerge_convergent_clonotyperemove_nonproductive_CDR3aa
Dependencies:bitbit64clicliprcpp11crayondplyrgenericsgluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readrrlangstringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| a dataframe of wide format | all_sample_all_chain_all_metrics_wide_format_dataframe |
| a dataframe list to combine rowwise. | all_sample_all_chain_all_metrics_wide_format_dataframe_list |
| a list of dataframes | all_sample_all_chain_individual_metrics_dataframe_list |
| a dataframe of wide format | all_sample_IGH_chain_all_metrics_wide_format_dataframe |
| a dataframe list to combine rowwise. | all_sample_IGH_chain_all_metrics_wide_format_dataframe_list |
| a list of dataframes | all_sample_IGH_chain_individual_metrics_dataframe_list |
| 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 |
| a dataframe separated by chain name | chain_separated_dataframe |
| combine_all_sample_repertoire_metrics | combine_all_sample_repertoire_metrics |
| compute_repertoire_metrics_by_chain_name | compute_repertoire_metrics_by_chain_name |
| a dataframe where convergent clonotypes are merged | convergent_clonotype_merged_dataframe |
| Convert clonotype dataframe to immunarch format | format_clonotype_to_immunarch_style |
| get_item_name_x_sample_name_for_each_metric | get_item_name_x_sample_name_for_each_metric |
| An converted dataframe to immunarch format | immunarch_style_dataframe |
| Merge convergent clonotype | merge_convergent_clonotype |
| a dataframe with nonproductive CDR3aa removed | nonproductive_CDR3aa_removed_dataframe |
| Parse mixcr format | parse_mixcr |
| Parse trust4 format | parse_trust4 |
| Raw clonotype output from trust4 | raw_input_clonotype_dataframe |
| Clean the clonotype dataframe | remove_nonproductive_CDR3aa |
| summarize_convergence_function | summarize_convergence_function |
| summarize_repertoire_metrics | summarize_repertoire_metrics |
| Make variable names global to avoid CHECK notes | the global variables |
| a list of dataframe where convergent clonotypes are merged | the_divergent_clonotype_dataframe_list |