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| +-method | Combines 2 AbSeqCRep objects together for comparison |
| +-method | Combines a AbSeqCRep object with a AbSeqRep object together for comparison |
| +-method | Combines a AbSeqRep object with a AbSeqCRep object together for comparison |
| +-method | Combines 2 AbSeqRep objects together for comparison |
| .abundanceAnalysis | Conducts abundance analysis |
| .abundancePlot | Abundance distribution |
| .alignQualityHeatMaps | Plots all 5 alignment quality heatmaps |
| .allPrimerNames | Collect primer names from FASTA |
| .aminoAcidBar | Plots amino acid composition logo |
| .aminoAcidPlot | Composition logo plot |
| .analyzeUpstreamValidity | Plots the validity of upstream sequences |
| .annotAnalysis | Annotation analysis |
| .asRepertoireAlignLen | Accessor for 'alignlen' slot |
| .asRepertoireBitscore | Accessor for 'bitscore' slot |
| .asRepertoireChain | Accessor for 'chain' slot |
| .asRepertoireDir | Accessor for the 'outdir' slot |
| .asRepertoireList | Accessor for AbSeqCRep's list of AbSeqRep objects |
| .asRepertoireName | Accessor for the 'name' slot |
| .asRepertoirePrimer3 | Accessor for the 'primer3end' slot |
| .asRepertoirePrimer5 | Accessor for the 'primer5end' slot |
| .asRepertoireQueryStart | Accessor for 'qstart' slot |
| .asRepertoireSubjectStart | Accessor for 'sstart' slot |
| .asRepertoireUpstream | Accessor for the 'upstream' slot |
| .boxPlot | Creates a box plot |
| .calculateDInd | Calculates the "standard" diversity indices |
| .calculateDiversityEstimates | Calculates Lower Bound Estimates for unseen species and Common Diversity Indices from clonotype tables |
| .canonicalizeTitle | Convert file names to human friendly text |
| .capitalize | Helper function to capitalize the first letter of 'str' |
| .checkVert | Checks if abseqPy has a metadata line that suggests the orientation |
| .cloneDistHist | Marginal histogram of clonotypes (blue for shared, grey for total). The y axis is scaled by sqrt (but it doesn't really matter anyway, since we're stripping away the y-ticks) |
| .cloneDistMarginal | Marginal density graph of clonotypes (blue for shared, grey for total, purple for exclusive clones) |
| .clonotypeAnalysis | Comprehensive clonotype analyses |
| .collateReports | Collate all HTML reports into a single directory and cretate an entry 'index.html' file that redirects to all collated HTML files |
| .commonPrimerNames | Collect the intersection of all primer names within a collection of primer files |
| .correlationTest | Conducts pearson and spearman correlation analysis on dataframe |
| .distanceMeasure | Computes the distance between pariwise samples |
| .diversityAnalysis | Title Diversity analysis |
| .emptyPlot | Creates and returns an empty plot |
| .findRepertoires | Given a directory = <abseqPy_outputdir>/RESULT_DIR/, returns the directories (repositories) in 'directory'. That is, will not return any sample_vs_sample directories. This is done by asserting that a 'repository' must have an (analysis.params) file, and a summary.txt file. |
| .generateAllSpectratypes | Generates all FR/CDR spectratypes |
| .generateDelayedReport | Generates report for all samples in 'compare' |
| .generateReport | Generates HTML report from 'AbSeqRep' and 'AbSeqCRep' ojects |
| .getLineTypes | Helper function to return line types by importance based on provided CD/Fs regions |
| .getTotal | Get total number of samples (n) |
| .hmFromMatrix | Plots a plotly heatmap from provided matrix |
| .inferAnalyzed | Returns all samples found under 'sampleDirectory' |
| .loadMatrixFromDF | Given a dataframe with the columns "from", "to", and value.var, return a symmetric matrix (with diagonal values = diag). I.e. a call to isSymmetric(return_value_of_this_function) will always be TRUE. |
| .loadSamplesFromString | Loads AbSeqCRep or AbSeqRep objects from a list of sampleNames |
| .pairwiseComparison | Conduct all vs all pairwise comparison analyses |
| .plotCirclize | V-J association plot |
| .plotDist | Bar plotter |
| .plotDiversityCurves | Plots rarefaction, recapture, and de-dup plots for specified 'region' |
| .plotDuplication | Duplication level plot |
| .plotErrorDist | Plots the error distribution for each region: CDRs, FRs, IGV, IGD, and IGJ |
| .plotIGVErrors | Plots the error distribution for IGV germlines |
| .plotIGVUpstreamLenDist | Plot IGV family distribution for a given 'upstreamLengthRange' |
| .plotIGVUpstreamLenDistDetailed | Plots the detailed length distribution for IGV families |
| .plotPrimerIGVStatus | Plots, for a given 'category' and 'pend', the 'primer' IGV indelled distribution in a bar plot |
| .plotPrimerIntegrity | Plots the distribution of primer integrity for a given 'category' and 5' or 3' 'pend' |
| .plotRarefaction | Rarefaction plot |
| .plotRecapture | Plots capture-recapture |
| .plotSamples | Monolith AbSeq Plot function - the "driver" program |
| .plotSpectratype | Spectratype plotter |
| .plotUpstreamLength | Plot upstream distribution |
| .plotUpstreamLengthDist | Plot upstream sequence length distribution for upstream sequences (5'UTR or secretion signal) for a given 'upstreamLengthRange' |
| .primerAnalysis | Conducts primer specificity analysis |
| .prodDistPlot | Plots a distribution plot for different productivity analysis files |
| .productivityAnalysis | Conducts productivty analysis |
| .productivityPlot | Summary of productivity |
| .readSummary | Return value specifed by key from AbSeq's summary file |
| .regionAnalysis | Title Shows varying regions for a given clonotype defined by its CDR3 |
| .reportLBE | Reports abundance-based (Lower bound) diversity estimates using the Vegan package |
| .saveAs | Saves ggplot object as a Rdata file. |
| .scatterPlot | Title Creates a scatter plot |
| .scatterPlotComplex | Creates a complex scatter plot |
| .secretionSignalAnalysis | Secretion signal analysis |
| .substituteStringInFile | Substitutes the first occurance of 'key' with 'value' in 'filename' |
| .summarySE | Summary of dataframe |
| .topNDist | Title Clonotype table |
| .UTR5Analysis | 5' UTR analysis |
| .vennIntersection | Title Creates Venndiagram for clonotype intersection |
| AbSeqCRep | S4 class - AbSeqCompositeRepertoire analysis object |
| AbSeqCRep-class | S4 class - AbSeqCompositeRepertoire analysis object |
| AbSeqRep | S4 class - AbSeqRepertoire analysis object |
| AbSeqRep-class | S4 class - AbSeqRepertoire analysis object |
| abseqReport | Visualize all analysis conducted by abseqPy |
| report | Plots AbSeqRep or AbSeqCRep object to the specfied directory |
| report-method | Plots AbSeqRep or AbSeqCRep object to the specfied directory |