sequences.mutation.AA: Detect amino acid mutations in V-, FR- or CDR-regions
In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description Usage Arguments Details Author(s) References See Also Examples

This functions detects amino acid mutations in V-, FR- or CDR-regions and returns a data frame containing proportions of mutations from amino acid x to amino acid y.

sequences.mutation.AA(mutationtab = NULL, 
     sequence = c("V", "FR1", "FR2", "FR3", "CDR1", "CDR2"))
plotSequencesMutationAA(mutationAAtab = NULL, 
     showChange = c("no","hydropathy", "volume", "chemical"), title = NULL, PDF = NULL)

`mutationtab`	IMGT output table 7_V-REGION-mutation-and-AA-change-table(...).txt
`sequence`	Sequence region to be analyzed (V, FR1, FR2, FR3, CDR1, CDR2)
`mutationAAtab`	Output table of sequences.mutation.AA()
`showChange`	Shall hydropathy, volume, chemical or no changes be returned?
`title`	Title of the plot
`PDF`	PDF project name (see Details)

sequences.mutation.AA() returns a 20 x 20 data frame containing proportions of amino acid mutations in a given region. Original amino acids are in rows, mutated ones in columns.

plotSequencesMutationAA() returns a kind of heatmap containing proportion of amino acid changes and hydropathy, chemical or volume changes. Original amino acids are in rows, mutated ones in columns. The PDF character string should be only the project name (without ".pdf"). A figure called "PDF"_AA-mutation.pdf will be saved to the working directory.

Julia Bischof

IMGT/HighV-QUEST V-REGION mutation and AA change table: http://www.imgt.org/IMGT_vquest/share/textes/imgtvquest.html#mut-table

IMGT Index "Mutation": http://www.imgt.org/IMGTindex/mutation.php

sequences.mutation.AA, plotSequencesMutationAA,

sequences.mutation, sequences.mutation.base,

plotSequencesMutationBase

data(mutationtab)
V.mut.AA<-sequences.mutation.AA(mutationtab = mutationtab, sequence = "V")
## Not run: 
plotSequencesMutationAA(mutationAAtab = V.mut.AA, showChange = "hydropathy")

## End(Not run)