Man pages for tcR
Advanced Data Analysis of Immune Receptor Repertoires

AA_TABLETables with genetic code.
apply.symmApply function to every pair of data frames from a list.
assymetryNormalised log assymetry. columns with counts for clonesets.
beta.probList with assembling probabilities of beta chain TCRs.
bootstrap.tcrBootstrap for data frames in package tcR.
check.distributionCheck for adequaty of distrubution. space homeostasis.
cloneset.statsMiTCR data frame basic statistics.
codon.variantsFunctions for working with aminoacid sequences.
column.summaryColumns statistics.
contamination.statsContamination filtering.
convergence.indexCompute convergence characteristics of repertoires.
cosine.sharingShared repertoire analysis.
cosine.similaritySet and vector similarity measures.
dot-add.legendInternal function. Add legend to a grid of plots and remove...
dot-column.choiceChoose the right column.
dot-fix.listnamesFix names in lists.
dot-verbose.msgPrint the given message if second parameter is a TRUE.
entropyInformation measures.
entropy.segRepertoires' analysis using information measures applied to...
find.clonotypesFind target clonotypes and get columns' value corresponded to...
find.similar.sequencesFind similar sequences.
fix.allelesFix alleles / genes by removing allele information /...
gc.contentGC-content of a nucleotide sequences.
generate.kmersGenerate k-mers.
generate.tcrGenerate random nucleotide TCR sequences.
geneUsageGene usage.
get.all.substringsGet all substrings for the given sequence.
get.deletions.alphaCompute the number of deletions in MiTCR data frames.
get.inframesIn-frame / out-of-frame sequences filter.
get.kmersGet kmers from sequences.
gibbs.samplerGibbs Sampler.
group.clonotypesGet all unique clonotypes.
has.classCheck if a given object has a given class.
intersectClonesetsIntersection between sets of sequences or any elements.
inverse.simpsonDistribution evaluation.
kmer.profileProfile of sequences of equal length.
kmer.tableMake and manage the table of the most frequent k-mers.
matrixdiagcopyCopy the up-triangle matrix values to low-triangle.
matrixSubgroupsGet all values from the matrix corresponding to specific...
mutated.neighboursGet vertex neighbours.
mutation.networkMake mutation network for the given repertoire.
ozScoreOverlap Z-score.
parse.clonesetParse input table files with the immune receptor repertoire...
parse.folderParse input table files with immune receptor repertoire data.
pca2euclidCompute the Euclidean distance among principal components.
pca.segmentsPerform PCA on segments frequency data.
permutDistTestMonte Carlo permutation test for pairwise and one-vs-all-wise...
permutedfShuffling data frames.
rarefactionDiversity evaluation using rarefaction.
repDiversityGeneral function for the repertoire diversity estimation.
repLoadParse input files or folders with immune receptor repertoire...
repOverlapGeneral function for the repertoire overlap evaluation.
repSaveSave tcR data frames to disk as text files or gzipped text...
resampleResample data frame using values from the column with number...
revcompDNA reverse complementing and translation.
reverse.stringReverse given character vector by the given n-plets.
sample2DGet a sample from matrix with probabilities.
sample.clonesGet a random subset from a data.frame.
segments.alphabetsAlphabets of TCR and Ig gene segments.
segments.listSegment data. group attribute for vertices of a mutation network
set.pbSimple functions for manipulating progress bars.
set.people.vectorSet and get attributes of a mutation network related to...
set.rankSet new columns "Rank" and "Index".
shared.repertoireShared TCR repertoire managing and analysis
startmitcrStart MiTCR directly from the package.
tailbound.proportionProportions of specifyed subsets of clones.
top.crossPerform sequential cross starting from the top of a data...
top.funGet samples from a repertoire slice-by-slice or top-by-top...
twinsdataTwins alpha-beta chain data
vis.clonal.dynamicsVisualise clonal dynamics among time points.
vis.clonal.spaceVisualise occupied by clones homeostatic space among Samples...
vis.count.lenPlot a histogram of lengths.
vis.gene.usageHistogram of segments usage. for groups of observations.
vis.kmer.histogramPlot of the most frequent kmers.
vis.logoLogo - plots for amino acid and nucletide profiles.
vis.number.countPlot a histogram of counts.
vis.pcaPCA result visualisation
vis.radarlikeRadar-like / spider-like plots.
vis.rarefactionRarefaction statistics visualisation.
vis.shared.clonotypesVisualisation of shared clonotypes occurrences among... of top clones proportions.
tcR documentation built on March 25, 2019, 5:05 p.m.