targetingMatrix {BCellMA}R Documentation

Function to the calculation of the number of Nucleotids at three positions before and after a mutation

Description

Function to the calculation of the number of Nucleotids at three positions before and after a mutation

Usage

targetingMatrix(data_tab2, data_tab_germline, data_tab7)

Arguments

data_tab2

Column V_Region in th IMGT table 2

data_tab_germline

Output from function germlineReconstr()

data_tab7

Column V_Region in th IMGT table 7

Value

Result is a list of 8 matrices with the numbers of nucleotides at three positions before and after a mutation from A, T, C, and G, as well as in a mutated sequence and in the germline sequence

References

Spencer J. and Dunn-Walters DK. Hypermutation at A-T base pairs: the A nucleotidereplacement spectrum is affected by adjacent nucleotides and there is no reverse comple-mentary of sequences flanking muated A and T nucleotides.J Immunol, 175(8):5170 - 5177,2005.

Zuckerman NS., Hazanov H., Barak M., Edelman H., Hess S., Shcolnik H., Dunn-Walters D.,and Mehr R. Somatic hypermutation and antigen-driven selection of B cells are altered inautoimmune diseases.J Autoimmun, 35(4):325 - 335, 2010. doi: 10.1016/j.jaut.2010.07.004.

Examples

data(IMGTtab2)
data(IMGTtab7)
germline<-germlineReconstr(IMGTtab2$V_REGION, IMGTtab7$V_REGION)
data<-targetingMatrix(data_tab2=IMGTtab2, data_tab_germline=germline, data_tab7=IMGTtab7)
data

[Package BCellMA version 0.3.4 Index]