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R/Data.R
In dowser: B Cell Receptor Phylogenetics Toolkit
# Documentation and definitions for data and constants
#### Sysdata ####
# 1x20 vector of default amino acid hydropathy scores
# HYDROPATHY_KYTJ82
# 1x20 vector of default amino acid bulkiness scores
# BULKINESS_ZIMJ68
# 1x20 vector of default amino acid polarity scores
# POLARITY_GRAR74
# 1x7 vector of default amino acid pK values
# PK_EMBOSS
#### Data ####
#' Example AIRR database
#'
#' A small example database subset from Laserson and Vigneault et al, 2014.
#'
#' @format A data.frame with the following AIRR style columns:
#' \itemize{
#' \item \code{sequence_id}: Sequence identifier
#' \item \code{sequence_alignment}: IMGT-gapped observed sequence.
#' \item \code{germline_alignment_d_mask}: IMGT-gapped germline sequence with N, P and
#' D regions masked.
#' \item \code{v_call}: V region allele assignments.
#' \item \code{v_call_genotyped}: TIgGER corrected V region allele assignment.
#' \item \code{d_call}: D region allele assignments.
#' \item \code{j_call}: J region allele assignments.
#' \item \code{junction}: Junction region sequence.
#' \item \code{junction_length}: Length of the junction region in nucleotides.
#' \item \code{np1_length}: Combined length of the N and P regions proximal
#' to the V region.
#' \item \code{np2_length}: Combined length of the N and P regions proximal
#' to the J region.
#' \item \code{sample}: Sample identifier. Time in relation to vaccination.
#' \item \code{isotype}: Isotype assignment.
#' \item \code{duplicate_count}: Copy count (number of duplicates) of the sequence.
#' \item \code{clone_id}: Change-O assignment clonal group identifier.
#' }
#'
#' @seealso \link{ExampleDbChangeo} \link{ExampleClones}
#'
#' @references
#' \enumerate{
#' \item Laserson U and Vigneault F, et al. High-resolution antibody dynamics of
#' vaccine-induced immune responses.
#' Proc Natl Acad Sci USA. 2014 111:4928-33.
#' }
"ExampleAirr"
#' Example Change-O database
#'
#' A small example database subset from Laserson and Vigneault et al, 2014.
#'
#' @format A data.frame with the following Change-O style columns:
#' \itemize{
#' \item \code{SEQUENCE_ID}: Sequence identifier
#' \item \code{SEQUENCE_IMGT}: IMGT-gapped observed sequence.
#' \item \code{GERMLINE_IMGT_D_MASK}: IMGT-gapped germline sequence with N, P and
#' D regions masked.
#' \item \code{V_CALL}: V region allele assignments.
#' \item \code{V_CALL_GENOTYPED}: TIgGER corrected V region allele assignment.
#' \item \code{D_CALL}: D region allele assignments.
#' \item \code{J_CALL}: J region allele assignments.
#' \item \code{JUNCTION}: Junction region sequence.
#' \item \code{JUNCTION_LENGTH}: Length of the junction region in nucleotides.
#' \item \code{NP1_LENGTH}: Combined length of the N and P regions proximal
#' to the V region.
#' \item \code{NP2_LENGTH}: Combined length of the N and P regions proximal
#' to the J region.
#' \item \code{SAMPLE}: Sample identifier. Time in relation to vaccination.
#' \item \code{ISOTYPE}: Isotype assignment.
#' \item \code{DUPCOUNT}: Copy count (number of duplicates) of the sequence.
#' \item \code{CLONE}: Change-O assignment clonal group identifier.
#' }
#'
#' @seealso \link{ExampleAirr} \link{ExampleClones}
#'
#' @references
#' \enumerate{
#' \item Laserson U and Vigneault F, et al. High-resolution antibody dynamics of
#' vaccine-induced immune responses.
#' Proc Natl Acad Sci USA. 2014 111:4928-33.
#' }
"ExampleDbChangeo"
#' Example Ig lineage trees
#'
#' A tibble of Ig lineage trees generated from the \code{ExampleAirr} file
#'
#' @format A tibble of airrClone and phylo objects output by getTrees.
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{seqs}: Number of sequences
#' \item \code{trees}: List of phylo objects
#' }
#'
#' @seealso \link{ExampleClones}
"ExampleClones"
#' Example Ig lineage trees with biopsy reconstructions.
#'
#' Same as ExampleClones but with biopsies predicted at internal nodes
#'
#' @format A tibble of airrClone and phylo objects output by getTrees.
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{seqs}: Number of sequences
#' \item \code{trees}: List of phylo objects
#' }
#'
#' @seealso \link{BiopsyTrees}
"BiopsyTrees"
#' Example Ig lineage trees with isotype reconstructions.
#'
#' Same as ExampleClones but with isotypes predicted at internal nodes
#'
#' @format A tibble of airrClone and phylo objects output by getTrees.
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{seqs}: Number of sequences
#' \item \code{trees}: List of phylo objects
#' }
#'
#' @seealso \link{IsotypeTrees}
"IsotypeTrees"
#' Example Ig lineage trees sampled over time.
#'
#' Same as ExampleClones but with timepoint as a trait value
#'
#' @format A tibble of airrClone and phylo objects output by getTrees.
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{seqs}: Number of sequences
#' \item \code{trees}: List of phylo objects
#' }
#'
#' @seealso \link{TimeTrees}
"TimeTrees"
#' Example Change-O database
#'
#' A small example database subset from Turner, J. S. et al. Human germinal centres
#' engage memory and naive B cells after influenza vaccination. Nature 586, 127–132 (2020).
#'
#' @format A data.frame with the following Change-O style columns:
#' \itemize{
#' \item \code{sequence_id}: Sequence identifier
#' \item \code{sequence}: B cell sequence
#' \item \code{productive}: A logical indicating if the sequence is productive.
#' \item \code{v_call}: V region allele assignments.
#' \item \code{d_call}: D region allele assignments.
#' \item \code{j_call}: J region allele assignments.
#' \item \code{sequence_alignment}: Sequence alignment.
#' \item \code{germline_alignment}: Germline alignment without gaps.
#' \item \code{junction}: Junction
#' \item \code{juncation_aa}: Junction aa
#' \item \code{vj_inframe}: A logical to see if the vj genes are in frame
#' \item \code{stop_codon}: A indicator if there is a stop codon within the alignment
#' \item \code{locus}: Locus identifier.
#' \item \code{v_sequence_start}: Where the V gene starts
#' \item \code{v_sequence_end}: Where the V gene ends
#' \item \code{v_germline_start}: Where the V germline starts
#' \item \code{v_germline_end}: Where the V germline ends
#' \item \code{np1_length}: Length of np1
#' \item \code{d_sequence_start}: Where the D gene starts
#' \item \code{d_sequence_end}: Where the D gene ends
#' \item \code{d_germline_start}: Where the D germline starts
#' \item \code{d_germline_end}: Where the D germline ends
#' \item \code{np2_length}: Length of np2
#' \item \code{j_sequence_start}: Where the J gene starts
#' \item \code{j_sequence_end}: Where the J gene ends
#' \item \code{j_germline_start}: Where the J germline starts
#' \item \code{j_germline_end}: Where the J germline ends
#' \item \code{junction_length}: Length of the junction region in nucleotides.
#' \item \code{v_score}: V score
#' \item \code{v_identity}: Identity score of V
#' \item \code{v_support}: V support
#' \item \code{d_score}: D score
#' \item \code{d_identity}: D identity
#' \item \code{d_support}: D support
#' \item \code{j_score}: J score
#' \item \code{j_support}: J support
#' \item \code{j_identity}: J identity
#' \item \code{cell_id}: Cell identifier
#' \item \code{consensus_count}: Consensus count
#' \item \code{indels}: Logical if indels are present
#' \item \code{sequence_vdj}: VDJ sequence
#' \item \code{v_germ_start_vdj}: Where the V germline starts on the VDJ
#' \item \code{v_germ_end_vdj}: Where the V germline ends on the VDJ
#' \item \code{subject}: Subject identifier
#' \item \code{timepoint}: Day the sample was taken
#' \item \code{cell_type}: Type of cell
#' \item \code{replicate}: Replicate number
#' \item \code{clone_id}: Change-O assignment clonal group identifier.
#' \item \code{seq_type}: Identifier of data type (10x)
#' \item \code{vj_gene}: VJ gene
#' \item \code{vj_alt_gene}: Alternative VJ gene
#' \item \code{v_germline_length}: Length of the V germline segment
#' \item \code{d_germline_length}: Length of the D germline segment
#' \item \code{j_germline_lenght}: Length of the J germline segment
#' \item \code{germline_alignment_d_mask}: Germline alignment with gaps
#' }
"ExampleMixedDb"
#' Example Multiple Partition Trees
#'
#' A small example database subset from Turner, J. S. et al. Human germinal centres
#' engage memory and naive B cells after influenza vaccination. Nature 586, 127–132 (2020).
#'
#' @format A data.frame with the following Change-O style columns:
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{locus}: Locus identifier.
#' \item \code{seqs}: Number of sequences
#' \item \code{igphyml_partitioned_trees}: IgPhyML partitioned tree
#' \item \code{raxml_partitioned_trees}: RAxML partitioned tree
#' }
"ExampleMixedClones"
NULL
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# Documentation and definitions for data and constants
#### Sysdata ####
# 1x20 vector of default amino acid hydropathy scores
# HYDROPATHY_KYTJ82
# 1x20 vector of default amino acid bulkiness scores
# BULKINESS_ZIMJ68
# 1x20 vector of default amino acid polarity scores
# POLARITY_GRAR74
# 1x7 vector of default amino acid pK values
# PK_EMBOSS
#### Data ####
#' Example AIRR database
#'
#' A small example database subset from Laserson and Vigneault et al, 2014.
#'
#' @format A data.frame with the following AIRR style columns:
#' \itemize{
#' \item \code{sequence_id}: Sequence identifier
#' \item \code{sequence_alignment}: IMGT-gapped observed sequence.
#' \item \code{germline_alignment_d_mask}: IMGT-gapped germline sequence with N, P and
#' D regions masked.
#' \item \code{v_call}: V region allele assignments.
#' \item \code{v_call_genotyped}: TIgGER corrected V region allele assignment.
#' \item \code{d_call}: D region allele assignments.
#' \item \code{j_call}: J region allele assignments.
#' \item \code{junction}: Junction region sequence.
#' \item \code{junction_length}: Length of the junction region in nucleotides.
#' \item \code{np1_length}: Combined length of the N and P regions proximal
#' to the V region.
#' \item \code{np2_length}: Combined length of the N and P regions proximal
#' to the J region.
#' \item \code{sample}: Sample identifier. Time in relation to vaccination.
#' \item \code{isotype}: Isotype assignment.
#' \item \code{duplicate_count}: Copy count (number of duplicates) of the sequence.
#' \item \code{clone_id}: Change-O assignment clonal group identifier.
#' }
#'
#' @seealso \link{ExampleDbChangeo} \link{ExampleClones}
#'
#' @references
#' \enumerate{
#' \item Laserson U and Vigneault F, et al. High-resolution antibody dynamics of
#' vaccine-induced immune responses.
#' Proc Natl Acad Sci USA. 2014 111:4928-33.
#' }
"ExampleAirr"
#' Example Change-O database
#'
#' A small example database subset from Laserson and Vigneault et al, 2014.
#'
#' @format A data.frame with the following Change-O style columns:
#' \itemize{
#' \item \code{SEQUENCE_ID}: Sequence identifier
#' \item \code{SEQUENCE_IMGT}: IMGT-gapped observed sequence.
#' \item \code{GERMLINE_IMGT_D_MASK}: IMGT-gapped germline sequence with N, P and
#' D regions masked.
#' \item \code{V_CALL}: V region allele assignments.
#' \item \code{V_CALL_GENOTYPED}: TIgGER corrected V region allele assignment.
#' \item \code{D_CALL}: D region allele assignments.
#' \item \code{J_CALL}: J region allele assignments.
#' \item \code{JUNCTION}: Junction region sequence.
#' \item \code{JUNCTION_LENGTH}: Length of the junction region in nucleotides.
#' \item \code{NP1_LENGTH}: Combined length of the N and P regions proximal
#' to the V region.
#' \item \code{NP2_LENGTH}: Combined length of the N and P regions proximal
#' to the J region.
#' \item \code{SAMPLE}: Sample identifier. Time in relation to vaccination.
#' \item \code{ISOTYPE}: Isotype assignment.
#' \item \code{DUPCOUNT}: Copy count (number of duplicates) of the sequence.
#' \item \code{CLONE}: Change-O assignment clonal group identifier.
#' }
#'
#' @seealso \link{ExampleAirr} \link{ExampleClones}
#'
#' @references
#' \enumerate{
#' \item Laserson U and Vigneault F, et al. High-resolution antibody dynamics of
#' vaccine-induced immune responses.
#' Proc Natl Acad Sci USA. 2014 111:4928-33.
#' }
"ExampleDbChangeo"
#' Example Ig lineage trees
#'
#' A tibble of Ig lineage trees generated from the \code{ExampleAirr} file
#'
#' @format A tibble of airrClone and phylo objects output by getTrees.
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{seqs}: Number of sequences
#' \item \code{trees}: List of phylo objects
#' }
#'
#' @seealso \link{ExampleClones}
"ExampleClones"
#' Example Ig lineage trees with biopsy reconstructions.
#'
#' Same as ExampleClones but with biopsies predicted at internal nodes
#'
#' @format A tibble of airrClone and phylo objects output by getTrees.
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{seqs}: Number of sequences
#' \item \code{trees}: List of phylo objects
#' }
#'
#' @seealso \link{BiopsyTrees}
"BiopsyTrees"
#' Example Ig lineage trees with isotype reconstructions.
#'
#' Same as ExampleClones but with isotypes predicted at internal nodes
#'
#' @format A tibble of airrClone and phylo objects output by getTrees.
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{seqs}: Number of sequences
#' \item \code{trees}: List of phylo objects
#' }
#'
#' @seealso \link{IsotypeTrees}
"IsotypeTrees"
#' Example Ig lineage trees sampled over time.
#'
#' Same as ExampleClones but with timepoint as a trait value
#'
#' @format A tibble of airrClone and phylo objects output by getTrees.
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{seqs}: Number of sequences
#' \item \code{trees}: List of phylo objects
#' }
#'
#' @seealso \link{TimeTrees}
"TimeTrees"
#' Example Change-O database
#'
#' A small example database subset from Turner, J. S. et al. Human germinal centres
#' engage memory and naive B cells after influenza vaccination. Nature 586, 127–132 (2020).
#'
#' @format A data.frame with the following Change-O style columns:
#' \itemize{
#' \item \code{sequence_id}: Sequence identifier
#' \item \code{sequence}: B cell sequence
#' \item \code{productive}: A logical indicating if the sequence is productive.
#' \item \code{v_call}: V region allele assignments.
#' \item \code{d_call}: D region allele assignments.
#' \item \code{j_call}: J region allele assignments.
#' \item \code{sequence_alignment}: Sequence alignment.
#' \item \code{germline_alignment}: Germline alignment without gaps.
#' \item \code{junction}: Junction
#' \item \code{juncation_aa}: Junction aa
#' \item \code{vj_inframe}: A logical to see if the vj genes are in frame
#' \item \code{stop_codon}: A indicator if there is a stop codon within the alignment
#' \item \code{locus}: Locus identifier.
#' \item \code{v_sequence_start}: Where the V gene starts
#' \item \code{v_sequence_end}: Where the V gene ends
#' \item \code{v_germline_start}: Where the V germline starts
#' \item \code{v_germline_end}: Where the V germline ends
#' \item \code{np1_length}: Length of np1
#' \item \code{d_sequence_start}: Where the D gene starts
#' \item \code{d_sequence_end}: Where the D gene ends
#' \item \code{d_germline_start}: Where the D germline starts
#' \item \code{d_germline_end}: Where the D germline ends
#' \item \code{np2_length}: Length of np2
#' \item \code{j_sequence_start}: Where the J gene starts
#' \item \code{j_sequence_end}: Where the J gene ends
#' \item \code{j_germline_start}: Where the J germline starts
#' \item \code{j_germline_end}: Where the J germline ends
#' \item \code{junction_length}: Length of the junction region in nucleotides.
#' \item \code{v_score}: V score
#' \item \code{v_identity}: Identity score of V
#' \item \code{v_support}: V support
#' \item \code{d_score}: D score
#' \item \code{d_identity}: D identity
#' \item \code{d_support}: D support
#' \item \code{j_score}: J score
#' \item \code{j_support}: J support
#' \item \code{j_identity}: J identity
#' \item \code{cell_id}: Cell identifier
#' \item \code{consensus_count}: Consensus count
#' \item \code{indels}: Logical if indels are present
#' \item \code{sequence_vdj}: VDJ sequence
#' \item \code{v_germ_start_vdj}: Where the V germline starts on the VDJ
#' \item \code{v_germ_end_vdj}: Where the V germline ends on the VDJ
#' \item \code{subject}: Subject identifier
#' \item \code{timepoint}: Day the sample was taken
#' \item \code{cell_type}: Type of cell
#' \item \code{replicate}: Replicate number
#' \item \code{clone_id}: Change-O assignment clonal group identifier.
#' \item \code{seq_type}: Identifier of data type (10x)
#' \item \code{vj_gene}: VJ gene
#' \item \code{vj_alt_gene}: Alternative VJ gene
#' \item \code{v_germline_length}: Length of the V germline segment
#' \item \code{d_germline_length}: Length of the D germline segment
#' \item \code{j_germline_lenght}: Length of the J germline segment
#' \item \code{germline_alignment_d_mask}: Germline alignment with gaps
#' }
"ExampleMixedDb"
#' Example Multiple Partition Trees
#'
#' A small example database subset from Turner, J. S. et al. Human germinal centres
#' engage memory and naive B cells after influenza vaccination. Nature 586, 127–132 (2020).
#'
#' @format A data.frame with the following Change-O style columns:
#' \itemize{
#' \item \code{clone_id}: Clonal cluster
#' \item \code{data}: List of airrClone objects
#' \item \code{locus}: Locus identifier.
#' \item \code{seqs}: Number of sequences
#' \item \code{igphyml_partitioned_trees}: IgPhyML partitioned tree
#' \item \code{raxml_partitioned_trees}: RAxML partitioned tree
#' }
"ExampleMixedClones"
NULL
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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