# Advanced Data Analysis of Immune Receptor Repertoires

## Documentation for package ‘tcR’ version 2.2.4.1

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

## Help Pages

A B C D E F G H I J K L M O P R S T U V misc

## -- A --

AA_TABLE | Tables with genetic code.
AA_TABLE_REVERSED | Tables with genetic code.
add.pb | Simple functions for manipulating progress bars.
apply.asymm | Apply function to every pair of data frames from a list.
apply.symm | Apply function to every pair of data frames from a list.
assymetry | Normalised log assymetry.

## -- B --

barcodes.to.reads | Rearrange columns with counts for clonesets.
beta.prob | List with assembling probabilities of beta chain TCRs.
bootstrap.tcr | Bootstrap for data frames in package tcR.
bunch.translate | DNA reverse complementing and translation.

## -- C --

chao1 | Distribution evaluation.
check.distribution | Check for adequaty of distrubution.
clonal.proportion | Proportions of specifyed subsets of clones.
clonal.space.homeostasis | Clonal space homeostasis.
cloneset.stats | MiTCR data frame basic statistics.
clonotypescount | In-frame / out-of-frame sequences filter.
codon.variants | Functions for working with aminoacid sequences.
column.summary | Columns statistics.
contamination.stats | Contamination filtering.
convergence.index | Compute convergence characteristics of repertoires.
cosine.sharing | Shared repertoire analysis.
cosine.similarity | Set and vector similarity measures.
count.frames | In-frame / out-of-frame sequences filter.
count.inframes | In-frame / out-of-frame sequences filter.
count.outframes | In-frame / out-of-frame sequences filter.

## -- D --

decontamination | Contamination filtering.
diversity | Distribution evaluation.
downsample | Resample data frame using values from the column with number of clonesets.

## -- E --

entropy | Information measures.
entropy.seg | Repertoires' analysis using information measures applied to V- and J- segment frequencies.
exact.match | Find similar sequences.

## -- F --

find.clonotypes | Find target clonotypes and get columns' value corresponded to that clonotypes.
find.similar.sequences | Find similar sequences.
fix.alleles | Fix alleles / genes by removing allele information / unnecessary colons.
fix.genes | Fix alleles / genes by removing allele information / unnecessary colons.

## -- G --

gc.content | GC-content of a nucleotide sequences.
genealphabets | Alphabets of TCR and Ig gene segments.
generate.kmers | Generate k-mers.
generate.kmers.prob | Generate k-mers.
generate.tcr | Generate random nucleotide TCR sequences.
genesegments | Segment data.
geneUsage | Gene usage.
get.all.substrings | Get all substrings for the given sequence.
get.deletions.alpha | Compute the number of deletions in MiTCR data frames.
get.deletions.beta | Compute the number of deletions in MiTCR data frames.
get.frames | In-frame / out-of-frame sequences filter.
get.group.names | Set group attribute for vertices of a mutation network
get.inframes | In-frame / out-of-frame sequences filter.
get.kmer.column | Make and manage the table of the most frequent k-mers.
get.kmers | Get kmers from sequences.
get.outframes | In-frame / out-of-frame sequences filter.
get.people.names | Set and get attributes of a mutation network related to source people.
gibbs.sampler | Gibbs Sampler.
gini | Distribution evaluation.
gini.simpson | Distribution evaluation.
group.clonotypes | Get all unique clonotypes.

## -- H --

hamming.match | Find similar sequences.
has.class | Check if a given object has a given class.
horn.index | Set and vector similarity measures.
HUMAN_IGHD | Alphabets of TCR and Ig gene segments.
HUMAN_IGHJ | Alphabets of TCR and Ig gene segments.
HUMAN_IGHV | Alphabets of TCR and Ig gene segments.
HUMAN_IGKJ | Alphabets of TCR and Ig gene segments.
HUMAN_IGKV | Alphabets of TCR and Ig gene segments.
HUMAN_IGLJ | Alphabets of TCR and Ig gene segments.
HUMAN_IGLV | Alphabets of TCR and Ig gene segments.
HUMAN_TRAJ | Alphabets of TCR and Ig gene segments.
HUMAN_TRAV | Alphabets of TCR and Ig gene segments.
HUMAN_TRBD | Alphabets of TCR and Ig gene segments.
HUMAN_TRBJ | Alphabets of TCR and Ig gene segments.
HUMAN_TRBV | Alphabets of TCR and Ig gene segments.
HUMAN_TRBV_ALS | Alphabets of TCR and Ig gene segments.
HUMAN_TRBV_FAM | Alphabets of TCR and Ig gene segments.
HUMAN_TRBV_GEN | Alphabets of TCR and Ig gene segments.
HUMAN_TRBV_MITCR | Alphabets of TCR and Ig gene segments.
HUMAN_TRDD | Alphabets of TCR and Ig gene segments.
HUMAN_TRDJ | Alphabets of TCR and Ig gene segments.
HUMAN_TRDV | Alphabets of TCR and Ig gene segments.
HUMAN_TRGJ | Alphabets of TCR and Ig gene segments.
HUMAN_TRGV | Alphabets of TCR and Ig gene segments.

## -- I --

insertion.stats | Columns statistics.
intersectClonesets | Intersection between sets of sequences or any elements.
intersectCount | Intersection between sets of sequences or any elements.
intersectIndices | Intersection between sets of sequences or any elements.
intersectLogic | Intersection between sets of sequences or any elements.
inverse.simpson | Distribution evaluation.

## -- J --

jaccard.index | Set and vector similarity measures.
js.div | Information measures.
js.div.seg | Repertoires' analysis using information measures applied to V- and J- segment frequencies.

## -- K --

kl.div | Information measures.
kmer.profile | Profile of sequences of equal length.
kmer.table | Make and manage the table of the most frequent k-mers.
kmers.profile | Profile of sequences of equal length.

## -- L --

levenshtein.match | Find similar sequences.
loglikelihood | Log-likelihood.

## -- M --

MACMUL_TRBJ | Alphabets of TCR and Ig gene segments.
MACMUL_TRBV | Alphabets of TCR and Ig gene segments.
matrixdiagcopy | Copy the up-triangle matrix values to low-triangle.
matrixSubgroups | Get all values from the matrix corresponding to specific groups.
morisitas.index | Set and vector similarity measures.
MOUSE_IGHD | Alphabets of TCR and Ig gene segments.
MOUSE_IGHJ | Alphabets of TCR and Ig gene segments.
MOUSE_IGHV | Alphabets of TCR and Ig gene segments.
MOUSE_IGKJ | Alphabets of TCR and Ig gene segments.
MOUSE_IGKV | Alphabets of TCR and Ig gene segments.
MOUSE_IGLJ | Alphabets of TCR and Ig gene segments.
MOUSE_IGLV | Alphabets of TCR and Ig gene segments.
MOUSE_TRAJ | Alphabets of TCR and Ig gene segments.
MOUSE_TRAV | Alphabets of TCR and Ig gene segments.
MOUSE_TRBJ | Alphabets of TCR and Ig gene segments.
MOUSE_TRBV | Alphabets of TCR and Ig gene segments.
MOUSE_TRDD | Alphabets of TCR and Ig gene segments.
MOUSE_TRDJ | Alphabets of TCR and Ig gene segments.
MOUSE_TRDV | Alphabets of TCR and Ig gene segments.
MOUSE_TRGJ | Alphabets of TCR and Ig gene segments.
MOUSE_TRGV | Alphabets of TCR and Ig gene segments.
mutated.neighbours | Get vertex neighbours.
mutation.network | Make mutation network for the given repertoire.

## -- O --

overlap.coef | Set and vector similarity measures.
ozScore | Overlap Z-score.

## -- P --

parse.cloneset | Parse input table files with the immune receptor repertoire data.
parse.file | Parse input table files with immune receptor repertoire data.
parse.file.list | Parse input table files with immune receptor repertoire data.
parse.folder | Parse input table files with immune receptor repertoire data.
parse.immunoseq | Parse input table files with immune receptor repertoire data.
parse.immunoseq2 | Parse input table files with immune receptor repertoire data.
parse.immunoseq3 | Parse input table files with immune receptor repertoire data.
parse.imseq | Parse input table files with immune receptor repertoire data.
parse.migec | Parse input table files with immune receptor repertoire data.
parse.migmap | Parse input table files with immune receptor repertoire data.
parse.mitcr | Parse input table files with immune receptor repertoire data.
parse.mitcrbc | Parse input table files with immune receptor repertoire data.
parse.mixcr | Parse input table files with immune receptor repertoire data.
parse.tcr | Parse input table files with immune receptor repertoire data.
parse.vdjtools | Parse input table files with immune receptor repertoire data.
pca.segments | Perform PCA on segments frequency data.
pca.segments.2D | Perform PCA on segments frequency data.
pca2euclid | Compute the Euclidean distance among principal components.
permutDistTest | Monte Carlo permutation test for pairwise and one-vs-all-wise within- and inter-group differences in a set of repertoires.
permutedf | Shuffling data frames.
prop.sample | Resample data frame using values from the column with number of clonesets.

## -- R --

rarefaction | Diversity evaluation using rarefaction.
repDiversity | General function for the repertoire diversity estimation.
repLoad | Parse input files or folders with immune receptor repertoire data.
repOverlap | General function for the repertoire overlap evaluation.
repSave | Save tcR data frames to disk as text files or gzipped text files.
repseq.stats | MiTCR data frame basic statistics.
resample | Resample data frame using values from the column with number of clonesets.
revcomp | DNA reverse complementing and translation.
reverse.string | Reverse given character vector by the given n-plets.
reverse.translation | Functions for working with aminoacid sequences.

## -- S --

sample.clones | Get a random subset from a data.frame.
sample2D | Get a sample from matrix with probabilities.
segments.alphabets | Alphabets of TCR and Ig gene segments.
segments.list | Segment data.
set.group.vector | Set group attribute for vertices of a mutation network
set.index | Set new columns "Rank" and "Index".
set.pb | Simple functions for manipulating progress bars.
set.people.vector | Set and get attributes of a mutation network related to source people.
set.rank | Set new columns "Rank" and "Index".
shared.clones.count | Shared repertoire analysis.
shared.matrix | Shared TCR repertoire managing and analysis
shared.repertoire | Shared TCR repertoire managing and analysis
shared.representation | Shared repertoire analysis.
shared.summary | Shared repertoire analysis.
similarity | Set and vector similarity measures.
slice_fun | Get samples from a repertoire slice-by-slice or top-by-top and apply function to them.
spectratype | Spectratype
startmitcr | Start MiTCR directly from the package.

## -- T --

tailbound.proportion | Proportions of specifyed subsets of clones.
top.cross | Perform sequential cross starting from the top of a data frame.
top.cross.plot | Perform sequential cross starting from the top of a data frame.
top.cross.vec | Perform sequential cross starting from the top of a data frame.
top.fun | Get samples from a repertoire slice-by-slice or top-by-top and apply function to them.
top.proportion | Proportions of specifyed subsets of clones.
translated.nucl.sequences | Functions for working with aminoacid sequences.
tversky.index | Set and vector similarity measures.
twa | Twins alpha-beta chain data
twb | Twins alpha-beta chain data
twinsdata | Twins alpha-beta chain data

## -- U --

unpermutedf | Shuffling data frames.

## -- V --

vis.clonal.dynamics | Visualise clonal dynamics among time points.
vis.clonal.space | Visualise occupied by clones homeostatic space among Samples or groups.
vis.count.len | Plot a histogram of lengths.
vis.gene.usage | Histogram of segments usage.
vis.group.boxplot | Boxplot for groups of observations.
vis.heatmap | Heatmap.
vis.J.usage | Histogram of segments usage.
vis.kmer.histogram | Plot of the most frequent kmers.
vis.logo | Logo - plots for amino acid and nucletide profiles.
vis.number.count | Plot a histogram of counts.
vis.pca | PCA result visualisation
vis.radarlike | Radar-like / spider-like plots.
vis.rarefaction | Rarefaction statistics visualisation.
vis.shared.clonotypes | Visualisation of shared clonotypes occurrences among repertoires.
vis.top.proportions | Visualisation of top clones proportions.
vis.V.usage | Histogram of segments usage.

## -- misc --

.add.legend | Internal function. Add legend to a grid of plots and remove legend from all plots of a grid.
.column.choice | Choose the right column.
.fix.listnames | Fix names in lists.
.verbose.msg | Print the given message if second parameter is a TRUE.