Advanced Data Analysis of Immune Receptor Repertoires


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Documentation for package ‘tcR’ version 2.3.2

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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.