bcRep (version 1.3.6)

sequences.mutation.base: Statistics about silent mutations

Description

This function calculates a) proportions of silent mutations from nucleotide A to B and b) proportions of A, C, G and T/U from positions -3 to +3 around a mutation.

Usage

sequences.mutation.base(mutationtab = NULL, summarytab = NULL,  analyseEnvironment = FALSE, analyseMutation = TRUE, sequence = c("V", "FR1", "FR2", "FR3", "CDR1", "CDR2"), nrCores = 1)

plotSequencesMutationBase(mutationBaseTab = NULL, plotEnvironment = FALSE,  plotMutation = TRUE, colHeatmap = c("white","darkblue"), title = NULL, PDF = NULL)

Arguments

mutationtab

IMGT output table 7_V-REGION-mutation-and-AA-change-table(...).txt

summarytab

IMGT output table 1_Summary(...).txt

analyseEnvironment

Shall proportions of A, C, G and T/U from positions -3 to +3 around a mutation be analysed? (default: FALSE)

analyseMutation

Shall proportions of mutations from nucleotide A to B be analysed? (default: TRUE)

sequence

Sequence region to be analyzed (V, FR1, FR2, FR3, CDR1, CDR2)

nrCores

Number of cores to be used for parallel processing

mutationBaseTab

Output of sequences.mutation.base()

plotEnvironment

Shall proportions of A, C, G and T/U from positions -3 to +3 around a mutation be plotted? (default: FALSE)

plotMutation

Shall proportions of mutations from nucleotide A to B be plotted? (default: TRUE)

colHeatmap

Colours for the heatmap (default: c("white","darkblue"))

title

Title of the plot

PDF

PDF project name (see Details)

Details

This function calculates a) proportions of silent mutations from nucleotide A to B and b) proportions of A, C, G and T/U from positions -3 to +3 around a mutation. For case a) a matrix containing proportions of mutations is returned. In case b) a data frame containing positions in columns and base changes in rows is returned. Position 0 is the position where mutation occurs. Position -3 to -1 and +1 to +3 show proportions of bases next to the mutated position.

Function plotSequencesMutationBase() returns a heatmap or barplots for every base. The PDF character string should be only the project name (without ".pdf"). A figure called "PDF"_Base-mutation_mutated-position.pdf" and/or "PDF"_Base-mutation_environment.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.php

See Also

sequences.mutation.base, plotSequencesMutationBase,

sequences.mutation.AA, plotSequencesMutationAA,

sequences.mutation,

Examples

data(mutationtab)
data(summarytab)
V.base.mut<-sequences.mutation.base(mutationtab = mutationtab, summarytab = summarytab, 
     sequence = "V", nrCores = 1)

## Not run: 
# plotSequencesMutationBase(mutationBaseTab = V.base.mut, plotMutation = T)
# ## End(Not run)