Advanced Analysis of B Cell Receptor Repertoire Data


[Up] [Top]

Documentation for package ‘bcRep’ version 1.3.6

Help Pages

bcRep-package Advanced Analysis of B Cell Receptor Repertoire Data
aaDistribution Amino acid distribution of sequences
aaseqtab Summary of amino acid sequences of B cells of one individual
aaseqtab2 Summary of amino acid sequences of B cells of another individual
bcRep Advanced Analysis of B Cell Receptor Repertoire Data
clones Grouping sequences into clones
clones.allind B cell clones of 8 individuals
clones.CDR3Length CDR3 length distribution of clones
clones.filterFunctionality Filter for productive/unproductive clones
clones.filterJunctionFrame Filter for in-frame/out-of-frame clones
clones.filterSize Filter clones for their size
clones.giniIndex Gini index of clones
clones.IDlist Match sequence ID's and clone ID's
clones.ind Data frame: clones of one individual
clones.shared Shared clones between samples
clones.shared.summary Shared clones between samples
combineIMGT Combination of several IMGT output folders
compare.aaDistribution Compare amino acid distribution of different samples
compare.geneUsage Compare gene usage of different samples
compare.trueDiversity Compare richness or diversity of different samples
dist.PCoA Principal coordinate analysis (PCoA; multidimensional scaling [MDS]) of dissimilarity/distance indices
geneUsage Gene usage statistics
geneUsage.distance Dissimilarity/distance indices for gene usage data
mutationtab Summary of mutations cells
ntseqtab Summary of nucleotide sequences of B cells of one individual
plotAADistribution Amino acid distribution of sequences
plotClonesCDR3Length CDR3 length distribution of clones
plotClonesCopyNumber Copy number of clones
plotCompareAADistribution Compare amino acid distribution of different samples
plotCompareGeneUsage Compare gene usage of different samples
plotCompareTrueDiversity Compare richness or diversity of different samples
plotDistPCoA Principal coordinate analysis (PCoA; multidimensional scaling [MDS]) of dissimilarity/distance indices
plotGeneComb Gene/gene combinations
plotGeneUsage Gene usage statistics
plotSequencesMutationAA Detect amino acid mutations in V-, FR- or CDR-regions
plotSequencesMutationBase Statistics about silent mutations
plotTrueDiversity True diversity of sequences
readIMGT Read IMGT/HighV-QUEST output files
sequences.distance Dissimilarity/distance indices for sequence data
sequences.functionality Summary of functionality of sequences
sequences.geneComb Gene/gene combinations
sequences.getAnyFunctionality Filter for productive or unproductive sequences
sequences.getAnyJunctionFrame Filter for in-frame or out-of-frame sequences
sequences.getInFrames Filter for in-frame or out-of-frame sequences
sequences.getOutOfFrames Filter for in-frame or out-of-frame sequences
sequences.getProductives Filter for productive or unproductive sequences
sequences.getUnproductives Filter for productive or unproductive sequences
sequences.junctionFrame Summary of junction frames of sequences
sequences.mutation Basic statistics on mutations of sequences
sequences.mutation.AA Detect amino acid mutations in V-, FR- or CDR-regions
sequences.mutation.base Statistics about silent mutations
summarytab Summary information of B cells of one individual
trueDiversity True diversity of sequences
vgenes VH gene usage data