bcRep (version 1.3.3)

sequences.mutation.base: Base proportion nearby mutations

Description

This function calculates proportion of A, C, G and T from positions -3 to +3 around a mutation.

Usage

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

plotSequencesMutationBase(mutationBaseTab = NULL, 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

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()

title

Title of the plot

PDF

PDF project name (see Details)

Value

• sequences.mutation.base() returns a data frame containing positions in columns and base changes in rows.

Details

This function calculates proportion of A, C, G and T from positions -3 to +3 around a mutation. 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 barplots for every base. The PDF character string should be only the project name (without ".pdf"). A figure called "PDF"_Base-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.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)

plotSequencesMutationBase(mutationBaseTab = V.base.mut)