BCellMA (version 0.3.2)

targeting_motiv: Function to calculate the difference at three positions before and after a mutation to identify the hotspot motifs

Description

The change around the mutated nucleotide flanking three bases each is expressed as the difference (

Usage

targeting_motiv(data)

Arguments

data

Output from the function hotspotmutMat().

Value

Output is a list of four mutation environments A, C, T and G with the difference (

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)
targeting_motiv_data<-targeting_motiv(data)
targeting_motiv_data