| Type: | Package |
| Title: | Repertoire Analysis of the Detected Clonotype |
| Version: | 0.1.1 |
| 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. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.2.1 |
| Imports: | magrittr, readr, tidyr, tidyselect |
| Depends: | R (≥ 2.10) |
| Suggests: | rmarkdown, knitr |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2022-08-16 17:53:07 UTC; Andy |
| Author: | Lizhong Ding [aut, cre] |
| Maintainer: | Lizhong Ding <z82xh3f4r@mozmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2022-08-16 18:20:02 UTC |
rTCRBCRr: 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.
Author(s)
Maintainer: Lizhong Ding z82xh3f4r@mozmail.com
a dataframe of wide format
Description
The data frame must be generated from combine_all_sample_repertoire_metrics function
Usage
all_sample_IGH_chain_all_metrics_wide_format_dataframe
Format
A data frame with m rows and n variables:
Source
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
a dataframe list to combine rowwise.
Description
The element data frame must be generated from calculate_IGH_isotype_proportion function
Usage
all_sample_IGH_chain_all_metrics_wide_format_dataframe_list
Format
A list of data frames with m rows and n variables:
Source
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
a list of dataframes
Description
The list of data frames generated from get_item_name_x_sample_name_for_each_metric
Usage
all_sample_IGH_chain_individual_metrics_dataframe_list
Format
A list of data frame with m rows and n variables:
Source
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
a dataframe of wide format
Description
The data frame must be generated from combine_all_sample_repertoire_metrics function
Usage
all_sample_all_chain_all_metrics_wide_format_dataframe
Format
A data frame with m rows and n variables:
Source
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
a dataframe list to combine rowwise.
Description
The element data frame must be generated from compute_repertoire_metrics_by_chain_name function
Usage
all_sample_all_chain_all_metrics_wide_format_dataframe_list
Format
A list of data frames with m rows and n variables:
Source
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
a list of dataframes
Description
The list of data frames generated from get_item_name_x_sample_name_for_each_metric
Usage
all_sample_all_chain_individual_metrics_dataframe_list
Format
A list of data frame with m rows and n variables:
Source
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/list
Annotate chain name and isotype name
Description
Annotate chain name and isotype name
Usage
annotate_chain_name_and_isotype_name(input_dataframe)
Arguments
input_dataframe |
A dataframe of clonotype of immunarch format |
Value
A dataframe of clonotype of immunarch format
Examples
annotate_chain_name_and_isotype_name(nonproductive_CDR3aa_removed_dataframe)
calculate_IGH_isotype_proportion
Description
calculate_IGH_isotype_proportion
Usage
calculate_IGH_isotype_proportion(input_dataframe)
Arguments
input_dataframe |
a clonotype dataframe with chain name and isotype name information |
Value
a dataframe of count and proportion of isotypes of IGH chain.
Examples
calculate_IGH_isotype_proportion(convergent_clonotype_merged_dataframe)
calculate_repertoire_metrics
Description
calculate_repertoire_metrics
Usage
calculate_repertoire_metrics(named_species_vector)
Arguments
named_species_vector |
a named vector |
Value
a named vector
Examples
a_named_vector <- c("apple" = 1, "banana" = 3, "cranberry" = 7, "date" = 10)
calculate_repertoire_metrics(a_named_vector)
calibrate_proportion_by_clones
Description
calibrate_proportion_by_clones
Usage
calibrate_proportion_by_clones(a_dataframe)
Arguments
a_dataframe |
a dataframe |
Value
a dataframe
a dataframe separated by chain name
Description
an example dataframe separated by chain name
Usage
chain_separated_dataframe
Format
A data frame with m rows and n variables:
Source
https://en.wikipedia.org/wiki/T-cell_receptor
combine_all_sample_repertoire_metrics
Description
combine_all_sample_repertoire_metrics
Usage
combine_all_sample_repertoire_metrics(input_dataframe_list)
Arguments
input_dataframe_list |
a list of dataframes with repertoire metrics by chain name |
Value
a wide table with all samples' all chains' all repertoire metrics
Examples
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
Description
compute_repertoire_metrics_by_chain_name
Usage
compute_repertoire_metrics_by_chain_name(input_dataframe)
Arguments
input_dataframe |
a clonotype dataframe with chain name information |
Value
repertoire metrics by chain name.
Examples
compute_repertoire_metrics_by_chain_name(convergent_clonotype_merged_dataframe)
a dataframe where convergent clonotypes are merged
Description
an example dataframe where convergent clonotypes are merged
Usage
convergent_clonotype_merged_dataframe
Format
A data frame with m rows and n variables:
Source
https://www.frontiersin.org/articles/10.3389/fimmu.2019.02985/full
Convert clonotype dataframe to immunarch format
Description
Convert clonotype dataframe to immunarch format
Usage
format_clonotype_to_immunarch_style(input_dataframe, clonotyping_tool)
Arguments
input_dataframe |
a clonotype dataframe from an upstream clonotyping tool |
clonotyping_tool |
choose from c("mixcr, "trust") |
Value
a clonotype dataframe of immunarch format
Examples
format_clonotype_to_immunarch_style(raw_input_clonotype_dataframe, "trust")
get_item_name_x_sample_name_for_each_metric
Description
get_item_name_x_sample_name_for_each_metric
Usage
get_item_name_x_sample_name_for_each_metric(input_dataframe)
Arguments
input_dataframe |
a dataframe with repertoire metrics calculated for each item name |
Value
a list of dataframes that is one single repertoire metric for all items in all samples
Examples
get_item_name_x_sample_name_for_each_metric(all_sample_all_chain_all_metrics_wide_format_dataframe)
An converted dataframe to immunarch format
Description
An example dataframe converted to immunarch format
Usage
immunarch_style_dataframe
Format
A data frame with m rows and n variables:
Source
https://github.com/immunomind/immunarch/
Merge convergent clonotype
Description
Merge convergent clonotype
Usage
merge_convergent_clonotype(input_dataframe)
Arguments
input_dataframe |
A dataframe of clonotype of immunarch format |
Value
A dataframe of clonotype of immunarch format merge_convergent_clonotype_function(an_immunarch_format_clonotype_dataframe)
Examples
merge_convergent_clonotype(chain_separated_dataframe)
a dataframe with nonproductive CDR3aa removed
Description
an example dataframe with nonproductive CDR3aa removed
Usage
nonproductive_CDR3aa_removed_dataframe
Format
A data frame with m rows and n variables:
Source
https://mixcr.readthedocs.io/en/master/analyze.html
Parse mixcr format
Description
Parse mixcr format
Usage
parse_mixcr(input_clone_dataframe)
Arguments
input_clone_dataframe |
Generated from mixcr program |
Value
A dataframe of immunarch format
Parse trust4 format
Description
Parse trust4 format
Usage
parse_trust4(input_clone_dataframe)
Arguments
input_clone_dataframe |
Generated from trust4 program |
Value
A dataframe of immunarch format
Raw clonotype output from trust4
Description
An example dataframe for raw clonotype identified by trust4
Usage
raw_input_clonotype_dataframe
Format
A data frame with m rows and n variables:
Source
https://github.com/liulab-dfci/TRUST4
Clean the clonotype dataframe
Description
Clean the clonotype dataframe
Usage
remove_nonproductive_CDR3aa(input_dataframe)
Arguments
input_dataframe |
A dataframe of clonotype of immunarch format |
Value
A dataframe of clonotype of immunarch format
Examples
remove_nonproductive_CDR3aa(immunarch_style_dataframe)
summarize_convergence_function
Description
summarize_convergence_function
Usage
summarize_convergence_function(a_dataframe)
Arguments
a_dataframe |
a dataframe |
Value
a dataframe
summarize_repertoire_metrics
Description
summarize_repertoire_metrics
Usage
summarize_repertoire_metrics(one_sample_dataframe)
Arguments
one_sample_dataframe |
a dataframe of clonotype in immunarch format |
Value
a named vector
Make variable names global to avoid CHECK notes
Description
Global variables
a list of dataframe where convergent clonotypes are merged
Description
an list of example dataframes where convergent clonotypes are merged
Usage
the_divergent_clonotype_dataframe_list
Format
A list of data frame with m rows and n variables:
Source
https://www.frontiersin.org/articles/10.3389/fimmu.2019.02985/full