Man pages for matsengrp/sumrep
Summary statistics for B cell receptor (BCR) repertoires

binContinuousListsAsDiscreteDiscretize two lists of continuous data into mutual,...
bootstrapFastaResample DNA sequences from a fasta file with replacement,...
callPartisCall partis
checkColumnA wrapper of 'alakazam::checkColumns' that stops execution...
collapseAllelesIgnore allelic differences of common genes
collapseColonedListHere we use stringr::str_split to get empty strings after a...
compareAcidityDistributionsCompare the acidity distributions of two datasets
compareAliphaticIndexDistributionsCompare the distributions of aliphatic indices of two...
compareAromaticityDistributionsCompare the aromaticity distributions of two datasets
compareAtchleyFactorDistributionsCompare the distributions of Atchley factors for two datasets
compareBasicityDistributionsCompare the basicity distributions of two datasets
compareBulkinessDistributionsCompare the bulkiness distributions of two datasets
compareCategoricalDistributionsGet the l1 divergence of two categorical distributions,...
compareCDR3LengthDistributionsCompare the distribution of CDR3 lengths for two datasets
compareCDR3PairwiseDistanceDistributionsCompare levenshtein distance distributions of two CDR3...
compareChargeDistributionsCompare the charge distributions of two datasets
compareColdspotCountDistributionsCompare coldspot count distributions of two sets of mature...
compareCollessLikeIndicesCompare Colless-like indices for two phylogenetic trees
compareCopheneticIndicesCompare cophenetic indices for two phylogenetic trees
compareDeletionLengthsCompare the deletion length distributions of two datasets
compareDGene3PrimeDeletionLengthDistributionsCompare the D gene 3' deletion length distributions of two...
compareDGene5PrimeDeletionLengthDistributionsCompare the D gene 5' deletion length distributions of two...
compareDGeneDistributionsCompare D gene distribution between two repertoires
compareDistanceFromGermlineToSequenceDistributionsCompare Levenshtein distance distributions from naive...
compareDJInsertionMatricesCompare the transition matrices for DJ insertions for two...
compareGCContentDistributionsCompare the GC distributions of two lists of DNA sequences
compareGeneUsageCompare gene usage counts for two lists of genes
compareGermlineGeneDistributionsCompare germline V, D, or J gene usage for two repertoires
compareGRAVYDistributionsCompare the GRAVY distributions of two datasets
compareHillNumbersCompare one or multiple Hill numbers of two datasets. The...
compareHotspotCountDistributionsCompare hotspot count distributions of two sets of mature BCR...
compareInFramePercentagesCompare the percentage of in-frame sequences of two datasets
compareJGene5PrimeDeletionLengthDistributionsCompare the J gene 5' deletion length distributions of two...
compareJGeneDistributionsCompare J gene distribution between two repertoires
compareJointGeneDistributionsCompare joint gene distributions of two datasets
compareKideraFactorDistributionsCompare the distributions of Kidera factors for two datasets
compareMutabilityModelsCompare the mutability models of two datasets
compareNNDistanceDistributionsCompare kth nearest neighbor distance distributions of two...
comparePairwiseDistanceDistributionsCompare pairwise distance distributions of two lists of...
comparePerGeneMutationRatesCompare per gene mutation rates of two datasets
comparePerGenePerPositionMutationRatesCompare per gene per position mutation rates of two datasets
comparePolarityDistributionsCompare the polarity distributions of two datasets
comparePositionalDistanceBetweenMutationsDistributionsCompare the positional distance between mutations...
compareRepertoiresRun through a full repertoire comparison
compareSackinIndicesCompare Sackin's indices for two phylogenetic trees
compareSelectionEstimatesCompare selection estimates for two datasets
compareSubstitutionAndMutabilityModelsCompare the substitution and mutability models of two...
compareVDInsertionMatricesCompare the transition matrices for VD insertions for two...
compareVDJDistributionsCompare joint V, D, and J gene usage between two annotated...
compareVGene3PrimeDeletionLengthDistributionsCompare the V gene 3' deletion length distributions of two...
compareVGeneDistributionsCompare V gene distribution between two repertoires
compareVJInsertionMatricesCompare the transition matrices for VJ insertions for two...
convertNucleobasesToAminoAcidsConvert a vector of DNA strings to a strings of single-letter...
convertNucleobasesToAminoAcidsBySequenceConvert a single DNA sequence string to an amino acid...
determineComparisonMethodDetermine the comparison method for stringdistmatrix
doComparisonApply 'function_string' to inputs 'input_1' and 'input_2',...
doNNSubsamplingBatchStepCompute the nearest neighbor distribution of a sample of...
extractCDR3CodonStartPositionsExtract CDR3 codon start positions from partis-returned...
filterAminoAcidSequencesFilter amino acid sequences by removing any 'X'...
getAcidityDistributionGet a vector of acidity values for a set of an amino acid...
getAliphaticIndexGet the aliphatic index of a DNA sequence
getAliphaticIndexDistributionGet the distribution of aliphatic indices of a list of...
getAminoAcidDistributionCompute a table of counts for each amino acid in the list of...
getAminoAcidPropertiesGet a particular distribution of amino acid properties using...
getAndPrintComparisonPrint the result and elapsed time of a set of comparisons,...
getApproximateDistributionApproximate the distribution of 'summary_function' for 'dat'...
getApproximateNearestNeighborDistributionRuns a special approximation routine since nearest neighbor...
getAromaticityDistributionGet a vector of aromaticity values for a set of an amino acid...
getAtchleyFactorDistributionGet the distribution of a given Atchley factor for a vector...
getAtchleyFactorDistributionsGet a list of the distributions of each of the five Atchley...
getAutomaticAverageDivergenceEstimate the divergence by subsampling and averaging until a...
getAverageDivergenceEstimate a divergence by subsampling and averaging over the...
getBasicityDistributionGet a vector of basicity values for a set of an amino acid...
getBulkinessDistributionGet a vector of bulkiness values for a set of an amino acid...
getCDR3LengthDistributionGet the distribution of inferred length of CDR3 regions of...
getCDR3PairwiseDistanceDistributionGet a vector of CDR3 DNA strings of an annotated dataset
getChargeDistributionGet a vector of charge values for a set of an amino acid...
getColdspotCountGet the number of occurrences of AID coldspots in a column of...
getColdspotCountDistributionGet full or approximate distribution of coldspot counts for a...
getCollessLikeIndexCompute Colless-like index for the given tree
getColumnSequencesThis function attempts to access the provided column from the...
getColumnValuesA wrapper of 'alakazam::checkColumns' that stops execution...
getContinuousJSDivergenceByIntegrationCompute JS divergence for continuous samples
getCopheneticIndexCompute cophenetic index for the given tree
getDeletionLengthsGet the requested deletion lengths of a dataset
getDGene3PrimeDeletionLengthDistributionGet the distribution of D gene 3' deletion lengths of a...
getDGene5PrimeDeletionLengthDistributionGet the distribution of D gene 5' deletion lengths of a...
getDistanceFromGermlineToSequenceDistributionGet the exact or approximate distribution of Levenshtein...
getDistanceMatrixGet distance matrix from stringdist
getDistancesFromGermlineToSequenceGet the exact distribution of Levenshtein distances from the...
getDistanceVectorGet sorted vector of pairwise distances
getDJInsertionLengthDistributionGet the distribution of DJ insertion lengths of a dataset
getDJInsertionMatrixGet the Markov transition matrix for DJ insertions
getFullPartisAnnotationDo extended partis processing of annotations
getGCContentGet the GC content of each sequence in a vector of strings
getGCContentDistributionGet the GC content distribution of a list of DNA sequences
getGRAVYDistributionGet the distribution of GRAVY values from a list or vector of...
getGridDimsHandy automatic dimension retrieval given number of grid...
getHotspotCountGet the number of occurrences of AID hotspots in a column of...
getHotspotCountDistributionGet full or approximate distribution of coldspot counts for a...
getIgBlastAnnotationsGet IgBLAST annotations from an input fasta file
getInFramePercentageGet the percentage of sequences in a dataset which, after VDJ...
getInsertionLengthsGet the insertion lengths corresponding to a column of a...
getInsertionMatrixGet the Markov transition matrix for either VD or DJ...
getJGene3PrimeDeletionLengthDistributionGet the distribution of J gene 3' deletion lengths of a...
getJGene5PrimeDeletionLengthDistributionGet the distribution of J gene 5' deletion lengths of a...
getJointGeneTableGet table of combined V, D, and J usage frequencies
getJSDivergenceCompute the JS Divergence of two samples
getKideraFactorDistributionsGet distributions for each of the ten Kidera factors for a...
getKideraFactorsBySequenceGet the kidera factors of a single sequence. See the...
getMarkovMatrixConstructs a Markov matrix for a vector of DNA sequences
getMotifCountGet number of times a motif occurs in a set of one or more...
getMutabilityModelGet the inferred mutability model of a repetoire
getMutationInfoGet per-gene and per-gene-per-position mutation information...
getNameFromFunctionStringHelper function to get abbreviated summary names from getter...
getNearestNeighborDistancesGet sorted list of nearest neighbor distances
getNearestNeighborDistributionGet exact or approximate nearest neighbor distance...
getPairwiseDistanceDistributionGet an exact or approximate distribution of pairwise...
getPartisAnnotationsPerform sequence annotation with partis. This function does...
getPartisAnnotationsFromStringsRun partis annotate on vector or list of sequences directly...
getPartisPartitionsPerform clonal partitioning with partis
getPartisSimulationSimulate a dataset based on parameters from partis...
getPerGeneMutationRatesGet mutation rates of each gene from a 'mutation_rates'...
getPerGenePerPositionMutationRatesGet mutation rates by position of each gene from a...
getPolarityDistributionGet a vector of polarity values for a set of an amino acid...
getPositionalDistanceBetweenMutationsDistributionGet the distribution of positional distances between...
getPositionalDistancesBetweenMutationsBySequenceGet the positional distances between mutations given a single...
getSackinIndexCompute Sackin's index for the given tree
getSelectionEstimateGet selection estimates via the shazam Baseline models
getSequenceListFromFastaImport a vector of DNA sequence strings from a fasta file
getSpotCountGet number of times a set of motif (hot/cold)spots occur in a...
getSubstitutionModelGet the inferred substitution model of a repertoire
getSumOfAbsoluteDifferencesGet the mean absolute difference of two sequences
getUsageTableFromFullListGet usage table from full list of categorical variables, such...
getVDInsertionLengthDistributionGet the distribution of VD insertion lengths of a dataset
getVDInsertionMatrixGet the Markov transition matrix for VD insertions
getVGene3PrimeDeletionLengthDistributionGet the distribution of V gene 3' deletion lengths of a...
getVGene5PrimeDeletionLengthDistributionGet the distribution of V gene 5' deletion lengths of a...
getVJInsertionLengthDistributionThis calls the function for VD insertions since the AIRR...
getVJInsertionMatrixGet the Markov transition matrix for DJ insertions
hasStopCodonCheck if an amino acid sequence has a stop codon
hasUnrecognizedAminoAcidsCheck if an amino acid sequence has unrecognized codons
loadNewDatasetsLoad datasets that are not already in the workspace. The...
multiplotDisplay an array of ggplots within one figure
parsePythonDictionaryParse a python dictionary string into an R list
plotAcidityDistributionPlot the acidity distribution of one or more datasets
plotAliphaticIndexDistributionPlot the aliphatic index distribution of one or more datasets
plotAromaticityDistributionPlot the aromaticity distribution of one or more datasets
plotBasicityDistributionPlot the basicity distribution of one or more datasets
plotBulkinessDistributionPlot the bulkiness distribution of one or more datasets
plotCDR3LengthDistributionPlot the CDR3 length distribution of one or more datasets
plotCDR3PairwiseDistanceDistributionPlot the CDR3 pairwise distance distribution of one or more...
plotChargeDistributionPlot the charge distribution of one or more datasets
plotClusterSizeDistributionPlot the cluster size distribution of one or more datasets
plotColdspotCountDistributionPlot the coldspot count distribution of one or more datasets
plotDGene3PrimeDeletionLengthDistributionPlot the D gene 3' deletion length distribution of one or...
plotDGene5PrimeDeletionLengthDistributionPlot the D gene 5' deletion length distribution of one or...
plotDistanceFromGermlineToSequenceDistributionPlot the distance from naive to mature distribution of one or...
plotDistributionPlot a summary distribution of one or more datasets
plotDJInsertionLengthDistributionPlot the DJ insertion length distribution of one or more...
plotGCContentDistributionPlot the GC content distribution of one or more datasets
plotGRAVYDistributionPlot the GRAVY index distribution of one or more datasets
plotHotspotCountDistributionPlot the hotspot count distribution of one or more datasets
plotJGene3PrimeDeletionLengthDistributionPlot the J gene 3' deletion length distribution of one or...
plotJGene5PrimeDeletionLengthDistributionPlot the J gene 5' deletion length distribution of one or...
plotNearestNeighborDistributionPlot the nearest neighbor distribution of one or more...
plotPairwiseDistanceDistributionPlot the pairwise distance distribution of one or more...
plotPolarityDistributionPlot the polarity distribution of one or more datasets
plotPositionalDistanceBetweenMutationsDistributionPlot the distance between mutation distribution of one or...
plotUnivariateDistributionsGenerate a gridded plot of each univariate distribution...
plotVDInsertionLengthDistributionPlot the VD insertion length distribution of one or more...
plotVGene3PrimeDeletionLengthDistributionPlot the V gene 3' deletion length distribution of one or...
plotVGene5PrimeDeletionLengthDistributionPlot the V gene 5' deletion length distribution of one or...
plotVJInsertionLengthDistributionThis calls the function for VD insertions since the AIRR...
preventOutputOverwriteEnsure sumrep does not accidentally delete any previous...
readPartisAnnotationsGet partis annotations from the partis output directory. Some...
removeEmptyStringsRemove empty strings from a list or vector
resampleDataResample a dataset with replacement
runIgorRun igor shell script from R
standardizeListConvert lists of factors or vectors of characters into a...
subsampleSubsample a dataset
subsampleVectorSubsample a vector
subsetToQuantileRangeSubset a distribution to a given quantile range (mostly for...
matsengrp/sumrep documentation built on Sept. 10, 2019, 8:43 p.m.