sequences.mutation: Basic statistics on mutations of sequences

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description

This function summarizes the number of mutations of sequences. It gives also information about the number of silent and replacement mutations, R/S ratio, as well as mutation numbers, depending on functionality or junction frame distributions.

Usage

sequences.mutation(mutationtab = NULL, summarytab = NULL, 
     sequence = c("V", "FR1", "FR2", "FR3", "CDR1", "CDR2"), functionality = FALSE, 
     junctionFr = FALSE, rsRatio=FALSE,...)

Arguments

summarytab	IMGT/HighV-QUEST output 1_Summarytab(...).txt
mutationtab	IMGT/HighV-QUEST output 7_V-REGION-mutation-and-AA-change-table(...).txt
sequence	One of V, FR1, FR2, FR3, CDR1, CDR2
functionality	TRUE: mutation vs. functionality will be returned (default: FALSE)
junctionFr	TRUE: mutation vs. junction frame usage will be returned, summarytab required (default: FALSE)
rsRatio	TRUE: R/S ratio will be returned (default: FALSE)
...

Details

IMGT/HighV-QUEST output file 7_V-REGION-mutation-and-AA-change-table(...).txt (mutationtab) is required as input. 1_Summarytab(...).txt (summarytab) is optional; if specified, junction frame information and in special for V sequences "V-REGION identity [nt]" can be returned. Mutations of V region, as well as FR1, 2, 3 and CDR1, 2 can be analyzed. rsRatio=T returns the ratio of replacement and silent mutations per sequence. Sequences without silent or replacement mutation, will have a ratio of 0.

Value

Output is a list containing

Number_of_mutations	data frame with number of total mutations, replacement and silent mutations (optional: V sequences V-REGION identity [nt], R/S ratio)
Functionality	Proportions of mutations and no mutations in productive and unproductive sequences (optional)
Junction_frame	Proportions of mutations and no mutations in in-frame and out-of-frame sequences (optional)
RS_ratio	Ratio of replacement and silent mutations (optional)

Author(s)

Julia Bischof

References

IMGT/HighV-QUEST V-REGION mutation and AA change table: http://www.imgt.org/IMGT_vquest/share/textes/imgtvquest.html#mut-table

IMGT Index "Mutation": http://www.imgt.org/IMGTindex/mutation.php

Examples

data(mutationtab)
data(summarytab)
V.mutation<-sequences.mutation(mutationtab = mutationtab, summarytab = summarytab, 
     sequence = "V", junctionFr = TRUE, rsRatio=TRUE)
CDR1.mutation<-sequences.mutation(mutationtab = mutationtab, sequence = "CDR1",
     functionality=TRUE)
par(mar=c(18,5,5,3))
barplot(as.numeric(CDR1.mutation$Functionality[,1]),
     names=rownames(CDR1.mutation$Functionality),
     ylab="proportion",main="Mutation vs. Functionality",las=3)

Example output

sh: 1: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Could not detect number of cores, defaulting to 1.

bcRep documentation built on May 2, 2019, 5:14 a.m.