targeting_motive_plot {BCellMA}R Documentation

Polt of the difference at three positions before and after a mutation to identify the hotspot motifs.

Description

The the difference (

Usage

targeting_motive_plot(pwm, xaxis = TRUE, yaxis = TRUE, xfontsize = 15,
  yfontsize = 15, xlim)

Arguments

pwm

Result of the function hotspot().

xaxis

Accept TRUE/FALSE parameter. TRUE draw X-axis.

yaxis

Accept TRUE/FALSE parameter. TRUE draw Y-axis.

xfontsize

The plot size of the X-axis.

yfontsize

The plot size of the Y-axis.

xlim

Limit of the drowed Y-axis.

Value

Output is plot the sequence logos around the mutation.

Note

The Function are based on functions from package segLogo.

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.

Bembom O. seqLogo: Sequence logos for DNA sequence alignments, Status 10.08.2016. URLhttp://www.bioconductor.org/packages/release/bioc/html/seqLogo.html.

Schneider TD. and Stephens RM. Sequence logos: a new way to display consensus sequences.Nucleic Acids Res, 18(20):6097 - 6100, 1990.

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_motive_plot(targeting_motiv_data$A, xfontsize = 15, yfontsize = 15, xlim=60 )


[Package BCellMA version 0.3.4 Index]