targetingMatrix: Function to the calculation of the number of Nucleotids at...

In BCellMA: B Cell Receptor Somatic Hyper Mutation Analysis

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

BCellMA documentation built on May 1, 2019, 7:58 p.m.