BCellMA: B Cell Receptor Somatic Hyper Mutation Analysis
Version 0.3.4

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.

Browse man pages Browse package API and functions Browse package files

AuthorOlena Ohlei <olena.ohlei@student.uni-luebeck.de>
Date of publication2017-03-08 10:58:44
MaintainerOlena Ohlei <olena.ohlei@student.uni-luebeck.de>
LicenseGPL (>= 2)
Version0.3.4
URL https://www.r-project.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BCellMA")

Man pages

aa_cdr3_dist: Average frequency of nucleotide mutations resulting in amino...
aa_dist: Average frequency of nucleotide mutations resulting in amino...
aa_plot: Plot of average frequency of nucleotide mutations resulting...
gene_comb_funk: gene/gene ratios of two gene families
gene_comb_plot: Plot of gene/gene ratios of two gene families
germlineReconstr: Function to reconstruction of germline sequencies based on...
IMGTtab1: IMGT Table 1
IMGTtab2: IMGT Table 2
IMGTtab7: IMGT Table 7
IMGTtab8: IMGT Table 8
Klassen: Klassen
lengthCDR3: Frequency distribution of the CDR3 length
na_funktion: The function to check for reconsrtruction errors
nucleotide_mutation: The frequencies of nucleotide mutations and the frequencies...
targetingMatrix: Function to the calculation of the number of Nucleotids at...
targeting_motiv: Function to calculate the difference at three positions...
targeting_motive_plot: Polt of the difference at three positions before and after a...

Functions

IMGTtab1 Man page
IMGTtab2 Man page
IMGTtab7 Man page
IMGTtab8 Man page
Klassen Man page
aa_cdr3_dist Man page Source code
aa_dist Man page Source code
aa_plot Man page Source code
aa_zaehlen2 Source code
aa_zaehlen2_CDR3 Source code
addLetter Source code
gene_comb_funk Man page Source code
gene_comb_plot Man page Source code
germlineReconstr Man page Source code
lengthCDR3 Man page Source code
letterA Source code
letterC Source code
letterG Source code
letterT Source code
lettersPlot_minus Source code
na_funktion Man page Source code
nucleotide_mutation Man page Source code
targetingMatrix Man page Source code
targeting_motiv Man page Source code
targeting_motive_plot Man page Source code

Files

inst
inst/doc
inst/doc/vignette.Rmd
inst/doc/vignette.R
inst/doc/vignette.html
NAMESPACE
data
data/IMGTtab2.rda
data/IMGTtab8.rda
data/IMGTtab1.rda
data/IMGTtab7.rda
data/Klassen.rda
data/datalist
R
R/aa_plot.R
R/targeting_motive_plot.R
R/targeting_motiv.R
R/na_funktion.R
R/gene_comb_funk.R
R/targetingMatrix.R
R/data.R
R/aa_cdr3_dist.R
R/aa_zaehlen2.R
R/intern.R
R/aa_zaehlen2_CDR3.R
R/nucleotide_matation.R
R/lengthCDR3.R
R/gene_comb_plot.R
R/germlineReconstr.R
R/aa_dist.R
R/lettersPlot_minus.R
vignettes
vignettes/vignette.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/aa_dist.Rd
man/na_funktion.Rd
man/aa_plot.Rd
man/gene_comb_plot.Rd
man/IMGTtab1.Rd
man/gene_comb_funk.Rd
man/targeting_motive_plot.Rd
man/IMGTtab8.Rd
man/IMGTtab2.Rd
man/IMGTtab7.Rd
man/targeting_motiv.Rd
man/nucleotide_mutation.Rd
man/aa_cdr3_dist.Rd
man/germlineReconstr.Rd
man/targetingMatrix.Rd
man/Klassen.Rd
man/lengthCDR3.Rd
BCellMA documentation built on May 19, 2017, 7:47 a.m.