Function reference • LymphoSeqTest

All functions

aggreateSeq(): Group productive sequences by repertoire

alignSeq(): Align multiple sequences

bhattacharyyaCoefficient(): Bhattacharyya coefficient

chordDiagramVDJ(): Chord diagram of VJ or DJ gene associations

clonalRelatedness(): Clonal relatedness

clonality(): Clonality

cloneTrack(): Clone tracking plot

commonSeqs(): Common sequences in two or more repertoire_ids

commonSeqsBar(): Common sequences bar plot

commonSeqsPlot(): Common sequences plot

commonSeqsVenn(): Common sequences Venn diagram

countKmer(): Find kmers and its counts

differentialAbundance(): Differential abundance analysis

exportFasta(): Export sequences in fasta format

geneFreq(): Gene frequencies

getGliphTable(): Group productive sequences by repertoire

getLorenz(): Calculate Lorenz curve

getRelatedness(): Calculate relatedness

lorenzCurve(): Lorenz curve

pairwisePlot(): Pairwise comparison plot

percentSI(): Percent similarity index

phyloTree(): Create phylogenetic tree

plotAlignment(): Visualize multiple sequence alignment of CDR3 sequences

plotRarefactionCurve(): Plot rarefication and extrapolation curves for samples

plotTrack(): Plot clone

plotTrackSingular() highlightPlot(): Highlight clones

productiveSeq(): Productive sequences

readGliph(): Read GLIPH files

readImmunoSeq() getStandard() readFiles() iReceptorFormat(): Read ImmunoSeq files

removeSeq(): Remove sequence

runINext(): Run iNEXT on repertoire_ids

scoringMatrix(): Bhattacharyya, Similarity, Sorensen, or PSI matrix

searchDB(): Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity from iReceptor2

searchIreceptor(): Search for T cell receptor beta CDR3 amino acid sequences in iReceptor

searchPublished(): Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity

searchSeq() findSeq(): Search for a sequence

seqMatrix(): Sequence matrix

similarityScore(): Similarity score

sorensenIndex(): Sorensen index

summarySeq(): Get summary statistics for each repertoire_id in the analysis

topFreq(): Top frequencies

topSeqs(): Top sequences

topSeqsPlot(): Cumulative frequency bar plot of top sequences

uniqueSeqs(): Unique sequences