bcRep (version 1.3.2)

sequences.mutation.AA: Detect amino acid mutations in V-, FR- or CDR-regions

Description

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.

Usage

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)

Arguments

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)

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.

References

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.html

See Also

sequences.mutation.AA, plotSequencesMutationAA,

sequences.mutation, sequences.mutation.base,

plotSequencesMutationBase

Examples

data(mutationtab)
V.mut.AA<-sequences.mutation.AA(mutationtab = mutationtab, sequence = "V")
plotSequencesMutationAA(mutationAAtab = V.mut.AA, showChange = "hydropathy")