Man pages for tcR
Advanced Data Analysis of Immune Receptor Repertoires
| AA_TABLE | Tables with genetic code. |
| apply.symm | Apply function to every pair of data frames from a list. |
| assymetry | Normalised log assymetry. |
| 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. |
| check.distribution | Check for adequaty of distrubution. |
| clonal.space.homeostasis | Clonal space homeostasis. |
| cloneset.stats | MiTCR data frame basic statistics. |
| 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. |
| dot-add.legend | Internal function. Add legend to a grid of plots and remove... |
| dot-column.choice | Choose the right column. |
| dot-fix.listnames | Fix names in lists. |
| dot-verbose.msg | Print the given message if second parameter is a TRUE. |
| entropy | Information measures. |
| entropy.seg | Repertoires' analysis using information measures applied to... |
| find.clonotypes | Find target clonotypes and get columns' value corresponded to... |
| find.similar.sequences | Find similar sequences. |
| fix.alleles | Fix alleles / genes by removing allele information /... |
| gc.content | GC-content of a nucleotide sequences. |
| generate.kmers | Generate k-mers. |
| generate.tcr | Generate random nucleotide TCR sequences. |
| 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.inframes | In-frame / out-of-frame sequences filter. |
| get.kmers | Get kmers from sequences. |
| gibbs.sampler | Gibbs Sampler. |
| group.clonotypes | Get all unique clonotypes. |
| has.class | Check if a given object has a given class. |
| intersectClonesets | Intersection between sets of sequences or any elements. |
| inverse.simpson | Distribution evaluation. |
| kmer.profile | Profile of sequences of equal length. |
| kmer.table | Make and manage the table of the most frequent k-mers. |
| loglikelihood | Log-likelihood. |
| matrixdiagcopy | Copy the up-triangle matrix values to low-triangle. |
| matrixSubgroups | Get all values from the matrix corresponding to specific... |
| mutated.neighbours | Get vertex neighbours. |
| mutation.network | Make mutation network for the given repertoire. |
| ozScore | Overlap Z-score. |
| parse.cloneset | Parse input table files with the immune receptor repertoire... |
| parse.folder | Parse input table files with immune receptor repertoire data. |
| pca2euclid | Compute the Euclidean distance among principal components. |
| pca.segments | Perform PCA on segments frequency data. |
| permutDistTest | Monte Carlo permutation test for pairwise and one-vs-all-wise... |
| permutedf | Shuffling data frames. |
| rarefaction | Diversity evaluation using rarefaction. |
| repDiversity | General function for the repertoire diversity estimation. |
| repLoad | Parse input files or folders with immune receptor repertoire... |
| repOverlap | General function for the repertoire overlap evaluation. |
| repSave | Save tcR data frames to disk as text files or gzipped text... |
| resample | Resample data frame using values from the column with number... |
| revcomp | DNA reverse complementing and translation. |
| reverse.string | Reverse given character vector by the given n-plets. |
| sample2D | Get a sample from matrix with probabilities. |
| sample.clones | Get a random subset from a data.frame. |
| 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.pb | Simple functions for manipulating progress bars. |
| set.people.vector | Set and get attributes of a mutation network related to... |
| set.rank | Set new columns "Rank" and "Index". |
| shared.repertoire | Shared TCR repertoire managing and analysis |
| spectratype | Spectratype |
| startmitcr | Start MiTCR directly from the package. |
| tailbound.proportion | Proportions of specifyed subsets of clones. |
| top.cross | Perform sequential cross starting from the top of a data... |
| top.fun | Get samples from a repertoire slice-by-slice or top-by-top... |
| twinsdata | Twins alpha-beta chain data |
| vis.clonal.dynamics | Visualise clonal dynamics among time points. |
| vis.clonal.space | Visualise occupied by clones homeostatic space among Samples... |
| 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.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... |
| vis.top.proportions | Visualisation of top clones proportions. |
