sequences.mutation.base: Statistics about silent mutations

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

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.

Author(s)

Julia Bischof

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)

bcRep documentation built on May 2, 2019, 5:14 a.m.