# Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

## Documentation for package ‘abseqR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

+-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