| Title: | Repertoire Analysis of the Detected Clonotype |
|---|---|
| Description: | 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: | Lizhong Ding [aut, cre] |
| Maintainer: | Lizhong Ding <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.1.1 |
| Built: | 2024-12-01 08:11:35 UTC |
| Source: | CRAN |
The data frame must be generated from combine_all_sample_repertoire_metrics function
all_sample_all_chain_all_metrics_wide_format_dataframeall_sample_all_chain_all_metrics_wide_format_dataframe
A data frame with m rows and n variables:
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
The element data frame must be generated from compute_repertoire_metrics_by_chain_name function
all_sample_all_chain_all_metrics_wide_format_dataframe_listall_sample_all_chain_all_metrics_wide_format_dataframe_list
A list of data frames with m rows and n variables:
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
The list of data frames generated from get_item_name_x_sample_name_for_each_metric
all_sample_all_chain_individual_metrics_dataframe_listall_sample_all_chain_individual_metrics_dataframe_list
A list of data frame with m rows and n variables:
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
The data frame must be generated from combine_all_sample_repertoire_metrics function
all_sample_IGH_chain_all_metrics_wide_format_dataframeall_sample_IGH_chain_all_metrics_wide_format_dataframe
A data frame with m rows and n variables:
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
The element data frame must be generated from calculate_IGH_isotype_proportion function
all_sample_IGH_chain_all_metrics_wide_format_dataframe_listall_sample_IGH_chain_all_metrics_wide_format_dataframe_list
A list of data frames with m rows and n variables:
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
The list of data frames generated from get_item_name_x_sample_name_for_each_metric
all_sample_IGH_chain_individual_metrics_dataframe_listall_sample_IGH_chain_individual_metrics_dataframe_list
A list of data frame with m rows and n variables:
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
Annotate chain name and isotype name
annotate_chain_name_and_isotype_name(input_dataframe)annotate_chain_name_and_isotype_name(input_dataframe)
input_dataframe |
A dataframe of clonotype of immunarch format |
A dataframe of clonotype of immunarch format
annotate_chain_name_and_isotype_name(nonproductive_CDR3aa_removed_dataframe)annotate_chain_name_and_isotype_name(nonproductive_CDR3aa_removed_dataframe)
calculate_IGH_isotype_proportion
calculate_IGH_isotype_proportion(input_dataframe)calculate_IGH_isotype_proportion(input_dataframe)
input_dataframe |
a clonotype dataframe with chain name and isotype name information |
a dataframe of count and proportion of isotypes of IGH chain.
calculate_IGH_isotype_proportion(convergent_clonotype_merged_dataframe)calculate_IGH_isotype_proportion(convergent_clonotype_merged_dataframe)
calculate_repertoire_metrics
calculate_repertoire_metrics(named_species_vector)calculate_repertoire_metrics(named_species_vector)
named_species_vector |
a named vector |
a named vector
a_named_vector <- c("apple" = 1, "banana" = 3, "cranberry" = 7, "date" = 10) calculate_repertoire_metrics(a_named_vector)a_named_vector <- c("apple" = 1, "banana" = 3, "cranberry" = 7, "date" = 10) calculate_repertoire_metrics(a_named_vector)
calibrate_proportion_by_clones
calibrate_proportion_by_clones(a_dataframe)calibrate_proportion_by_clones(a_dataframe)
a_dataframe |
a dataframe |
a dataframe
an example dataframe separated by chain name
chain_separated_dataframechain_separated_dataframe
A data frame with m rows and n variables:
https://en.wikipedia.org/wiki/T-cell_receptor
combine_all_sample_repertoire_metrics
combine_all_sample_repertoire_metrics(input_dataframe_list)combine_all_sample_repertoire_metrics(input_dataframe_list)
input_dataframe_list |
a list of dataframes with repertoire metrics by chain name |
a wide table with all samples' all chains' all repertoire metrics
combine_all_sample_repertoire_metrics(all_sample_all_chain_all_metrics_wide_format_dataframe_list) combine_all_sample_repertoire_metrics(all_sample_IGH_chain_all_metrics_wide_format_dataframe_list)combine_all_sample_repertoire_metrics(all_sample_all_chain_all_metrics_wide_format_dataframe_list) combine_all_sample_repertoire_metrics(all_sample_IGH_chain_all_metrics_wide_format_dataframe_list)
compute_repertoire_metrics_by_chain_name
compute_repertoire_metrics_by_chain_name(input_dataframe)compute_repertoire_metrics_by_chain_name(input_dataframe)
input_dataframe |
a clonotype dataframe with chain name information |
repertoire metrics by chain name.
compute_repertoire_metrics_by_chain_name(convergent_clonotype_merged_dataframe)compute_repertoire_metrics_by_chain_name(convergent_clonotype_merged_dataframe)
an example dataframe where convergent clonotypes are merged
convergent_clonotype_merged_dataframeconvergent_clonotype_merged_dataframe
A data frame with m rows and n variables:
https://www.frontiersin.org/articles/10.3389/fimmu.2019.02985/full
Convert clonotype dataframe to immunarch format
format_clonotype_to_immunarch_style(input_dataframe, clonotyping_tool)format_clonotype_to_immunarch_style(input_dataframe, clonotyping_tool)
input_dataframe |
a clonotype dataframe from an upstream clonotyping tool |
clonotyping_tool |
choose from c("mixcr, "trust") |
a clonotype dataframe of immunarch format
format_clonotype_to_immunarch_style(raw_input_clonotype_dataframe, "trust")format_clonotype_to_immunarch_style(raw_input_clonotype_dataframe, "trust")
get_item_name_x_sample_name_for_each_metric
get_item_name_x_sample_name_for_each_metric(input_dataframe)get_item_name_x_sample_name_for_each_metric(input_dataframe)
input_dataframe |
a dataframe with repertoire metrics calculated for each item name |
a list of dataframes that is one single repertoire metric for all items in all samples
get_item_name_x_sample_name_for_each_metric(all_sample_all_chain_all_metrics_wide_format_dataframe)get_item_name_x_sample_name_for_each_metric(all_sample_all_chain_all_metrics_wide_format_dataframe)
An example dataframe converted to immunarch format
immunarch_style_dataframeimmunarch_style_dataframe
A data frame with m rows and n variables:
https://github.com/immunomind/immunarch/
Merge convergent clonotype
merge_convergent_clonotype(input_dataframe)merge_convergent_clonotype(input_dataframe)
input_dataframe |
A dataframe of clonotype of immunarch format |
A dataframe of clonotype of immunarch format merge_convergent_clonotype_function(an_immunarch_format_clonotype_dataframe)
merge_convergent_clonotype(chain_separated_dataframe)merge_convergent_clonotype(chain_separated_dataframe)
an example dataframe with nonproductive CDR3aa removed
nonproductive_CDR3aa_removed_dataframenonproductive_CDR3aa_removed_dataframe
A data frame with m rows and n variables:
https://mixcr.readthedocs.io/en/master/analyze.html
Parse mixcr format
parse_mixcr(input_clone_dataframe)parse_mixcr(input_clone_dataframe)
input_clone_dataframe |
Generated from mixcr program |
A dataframe of immunarch format
Parse trust4 format
parse_trust4(input_clone_dataframe)parse_trust4(input_clone_dataframe)
input_clone_dataframe |
Generated from trust4 program |
A dataframe of immunarch format
An example dataframe for raw clonotype identified by trust4
raw_input_clonotype_dataframeraw_input_clonotype_dataframe
A data frame with m rows and n variables:
https://github.com/liulab-dfci/TRUST4
Clean the clonotype dataframe
remove_nonproductive_CDR3aa(input_dataframe)remove_nonproductive_CDR3aa(input_dataframe)
input_dataframe |
A dataframe of clonotype of immunarch format |
A dataframe of clonotype of immunarch format
remove_nonproductive_CDR3aa(immunarch_style_dataframe)remove_nonproductive_CDR3aa(immunarch_style_dataframe)
summarize_convergence_function
summarize_convergence_function(a_dataframe)summarize_convergence_function(a_dataframe)
a_dataframe |
a dataframe |
a dataframe
summarize_repertoire_metrics
summarize_repertoire_metrics(one_sample_dataframe)summarize_repertoire_metrics(one_sample_dataframe)
one_sample_dataframe |
a dataframe of clonotype in immunarch format |
a named vector
an list of example dataframes where convergent clonotypes are merged
the_divergent_clonotype_dataframe_listthe_divergent_clonotype_dataframe_list
A list of data frame with m rows and n variables:
https://www.frontiersin.org/articles/10.3389/fimmu.2019.02985/full