Man pages for abseqR
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

AbSeqCRep-classS4 class - AbSeqCompositeRepertoire analysis object
AbSeqRep-classS4 class - AbSeqRepertoire analysis object
abseqReportVisualize all analysis conducted by abseqPy
dot-abundanceAnalysisConducts abundance analysis
dot-abundancePlotAbundance distribution
dot-alignQualityHeatMapsPlots all 5 alignment quality heatmaps
dot-allPrimerNamesCollect primer names from FASTA
dot-aminoAcidBarPlots amino acid composition logo
dot-aminoAcidPlotComposition logo plot
dot-analyzeUpstreamValidityPlots the validity of upstream sequences
dot-annotAnalysisAnnotation analysis
dot-asRepertoireAlignLenAccessor for 'alignlen' slot
dot-asRepertoireBitscoreAccessor for 'bitscore' slot
dot-asRepertoireChainAccessor for 'chain' slot
dot-asRepertoireDirAccessor for the 'outdir' slot
dot-asRepertoireListAccessor for AbSeqCRep's list of AbSeqRep objects
dot-asRepertoireNameAccessor for the 'name' slot
dot-asRepertoirePrimer3Accessor for the 'primer3end' slot
dot-asRepertoirePrimer5Accessor for the 'primer5end' slot
dot-asRepertoireQueryStartAccessor for 'qstart' slot
dot-asRepertoireSubjectStartAccessor for 'sstart' slot
dot-asRepertoireUpstreamAccessor for the 'upstream' slot
dot-boxPlotCreates a box plot
dot-calculateDIndCalculates the "standard" diversity indices
dot-calculateDiversityEstimatesCalculates Lower Bound Estimates for unseen species and...
dot-canonicalizeTitleConvert file names to human friendly text
dot-capitalizeHelper function to capitalize the first letter of 'str'
dot-checkVertChecks if abseqPy has a metadata line that suggests the...
dot-cloneDistHistMarginal histogram of clonotypes (blue for shared, grey for...
dot-cloneDistMarginalMarginal density graph of clonotypes (blue for shared, grey...
dot-clonotypeAnalysisComprehensive clonotype analyses
dot-collateReportsCollate all HTML reports into a single directory and cretate...
dot-commonPrimerNamesCollect the intersection of all primer names within a...
dot-correlationTestConducts pearson and spearman correlation analysis on...
dot-distanceMeasureComputes the distance between pariwise samples
dot-diversityAnalysisTitle Diversity analysis
dot-emptyPlotCreates and returns an empty plot
dot-findRepertoiresGiven a directory = <abseqPy_outputdir>/RESULT_DIR/, returns...
dot-generateAllSpectratypesGenerates all FR/CDR spectratypes
dot-generateDelayedReportGenerates report for all samples in 'compare'
dot-generateReportGenerates HTML report from 'AbSeqRep' and 'AbSeqCRep' ojects
dot-getLineTypesHelper function to return line types by importance based on...
dot-getTotalGet total number of samples (n)
dot-hmFromMatrixPlots a plotly heatmap from provided matrix
dot-inferAnalyzedReturns all samples found under 'sampleDirectory'
dot-loadMatrixFromDFGiven a dataframe with the columns "from", "to", and...
dot-loadSamplesFromStringLoads AbSeqCRep or AbSeqRep objects from a list of...
dot-pairwiseComparisonConduct all vs all pairwise comparison analyses
dot-plotCirclizeV-J association plot
dot-plotDistBar plotter
dot-plotDiversityCurvesPlots rarefaction, recapture, and de-dup plots for specified...
dot-plotDuplicationDuplication level plot
dot-plotErrorDistPlots the error distribution for each region: CDRs, FRs, IGV,...
dot-plotIGVErrorsPlots the error distribution for IGV germlines
dot-plotIGVUpstreamLenDistPlot IGV family distribution for a given...
dot-plotIGVUpstreamLenDistDetailedPlots the detailed length distribution for IGV families
dot-plotPrimerIGVStatusPlots, for a given 'category' and 'pend', the 'primer' IGV...
dot-plotPrimerIntegrityPlots the distribution of primer integrity for a given...
dot-plotRarefactionRarefaction plot
dot-plotRecapturePlots capture-recapture
dot-plotSamplesMonolith AbSeq Plot function - the "driver" program
dot-plotSpectratypeSpectratype plotter
dot-plotUpstreamLengthPlot upstream distribution
dot-plotUpstreamLengthDistPlot upstream sequence length distribution for upstream...
dot-primerAnalysisConducts primer specificity analysis
dot-prodDistPlotPlots a distribution plot for different productivity analysis...
dot-productivityAnalysisConducts productivty analysis
dot-productivityPlotSummary of productivity
dot-readSummaryReturn value specifed by key from AbSeq's summary file
dot-regionAnalysisTitle Shows varying regions for a given clonotype defined by...
dot-reportLBEReports abundance-based (Lower bound) diversity estimates...
dot-saveAsSaves ggplot object as a Rdata file.
dot-scatterPlotTitle Creates a scatter plot
dot-scatterPlotComplexCreates a complex scatter plot
dot-secretionSignalAnalysisSecretion signal analysis
dot-substituteStringInFileSubstitutes the first occurance of 'key' with 'value' in...
dot-summarySESummary of dataframe
dot-topNDistTitle Clonotype table
dot-UTR5Analysis5' UTR analysis
dot-vennIntersectionTitle Creates Venndiagram for clonotype intersection
plus-AbSeqCRep-AbSeqCRep-methodCombines 2 AbSeqCRep objects together for comparison
plus-AbSeqCRep-AbSeqRep-methodCombines a AbSeqCRep object with a AbSeqRep object together...
plus-AbSeqRep-AbSeqCRep-methodCombines a AbSeqRep object with a AbSeqCRep object together...
plus-AbSeqRep-AbSeqRep-methodCombines 2 AbSeqRep objects together for comparison
reportPlots AbSeqRep or AbSeqCRep object to the specfied directory
abseqR documentation built on Nov. 1, 2018, 4:34 a.m.