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BCellMA (version 0.3.2)

B Cell Receptor Somatic Hyper Mutation Analysis

Description

Includes a set of functions to analyze for instance nucleotide frequencies as well as transition and transversion. Can reconstruct germline sequences based on the international ImMunoGeneTics information system (IMGT/HighV-QUEST) outputs, calculate and plot the difference (%) of nucleotides at 6 positions around a mutation to identify and characterize hotspot motifs as well as calculate and plot average mutation frequencies of nucleotide mutations resulting in amino acid substitution.

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Version

Install

install.packages('BCellMA')

Monthly Downloads

24

Version

0.3.2

License

GPL (>= 2)

Maintainer

Olena Ohlei

Last Published

November 29th, 2016

Functions in BCellMA (0.3.2)

aa_cdr3_dist

Average frequency of nucleotide mutations resulting in amino acid substitution in CDR3
nucleotide_mutation

The frequencies of nucleotide mutations and the frequencies of transition and transversion
germlineReconstr

Function to reconstruction of germline sequencies based on IMGT outputs.
aa_plot

Plot of average frequency of nucleotide mutations resulting in amino acid substitution
IMGTtab7

IMGT Table 7
aa_dist

Average frequency of nucleotide mutations resulting in amino acid substitution in FRs and CDRs
IMGTtab2

IMGT Table 2
na_funktion

The function to check for reconsrtruction errors
IMGTtab8

IMGT Table 8
Klassen

Klassen
targetingMatrix

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

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

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