Infers Novel Immunoglobulin Alleles from Sequencing Data

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Documentation for package ‘tigger’ version 1.1.0

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

Help Pages

AIRRDb	Example human immune repertoire data
cleanSeqs	Clean up nucleotide sequences
findNovelAlleles	Find novel alleles from repertoire sequencing data
findUnmutatedCalls	Determine which calls represent an unmutated allele
generateEvidence	Generate evidence
genotypeFasta	Return the nucleotide sequences of a genotype
GermlineIGHV	Human IGHV germlines
getMutatedPositions	Find the location of mutations in a sequence
getMutCount	Determine the mutation counts from allele calls
getPopularMutationCount	Find mutation counts for frequency sequences
inferGenotype	Infer a subject-specific genotype using a frequency method
inferGenotypeBayesian	Infer a subject-specific genotype using a Bayesian approach
insertPolymorphisms	Insert polymorphisms into a nucleotide sequence
plotGenotype	Show a colorful representation of a genotype
plotNovel	Visualize evidence of novel V alleles
readIgFasta	Read immunoglobulin sequences
reassignAlleles	Correct allele calls based on a personalized genotype
SampleDb	Example human immune repertoire data
SampleGenotype	Example genotype inferrence results
SampleGermlineIGHV	Example Human IGHV germlines
SampleNovel	Example novel allele detection results
selectNovel	Select rows containing novel alleles
sortAlleles	Sort allele names
subsampleDb	Subsample repertoire
tigger	tigger
updateAlleleNames	Update IGHV allele names
writeFasta	Write to a fasta file