sequences.functionality: Summary of functionality of sequences

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description

This function gives information about the proportion of productive and unproductive sequences.

Usage

sequences.functionality(data = NULL, relativeValues=TRUE, ...)

Arguments

data	Vector containing functionality information, e.g. taken from IMGT/HighV-QUEST output, e.g. 1_Summary(...).txt, 3_Nt-sequences(...).txt, 5_AA-sequences(...).txt
relativeValues	Shall relative or absolute values be returned? (default: TRUE)
...

Details

Productive sequences: include no stop codon and are in-frame

Unproductive sequences: include a stop codon and/or are out-of-frame

Value

Output is a data frame including proportions of productive and unproductive sequences, as well as proportion of sequences with unknown functionality.

Author(s)

Julia Bischof

References

IMGT/LIGM-DB labels: http://www.imgt.org/ligmdb/label

IMGT/HighV-QUEST definition of functionality: http://www.imgt.org/IMGTScientificChart/SequenceDescription/IMGTfunctionality.html#func

See Also

sequences.junctionFrame

Examples

data(summarytab)
funct<-sequences.functionality(data = summarytab$Functionality)
barplot(as.numeric(funct),xlab="",xlim=c(0,2),legend.text = colnames(funct),
     col=c("orange","darkblue","gray"),xaxt="n",main="Functionality",ylab="proportion")

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