bcRep (version 1.3.6)

sequences.junctionFrame: Summary of junction frames of sequences

Description

This function gives information about the proportion of in-frame and out-of-frame sequences.

Usage

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

Arguments

data

Vector containing junction frame information, e.g. taken from IMGT/HighV-QUEST output 1_Summary(...).txt

relativeValues

Shall relative or absolute values be returned? (default: TRUE)

...

Value

Output is a data frame including proportions of in-frame and out-of-frame sequences, as well as proportion of sequences without any information about junction frames.

Details

Junction: coding region of the V-J or V-D-J junction from 2nd CYS (position 104) to J-PHE or J-TRP (position 118) in an IG or TR V-DOMAIN (http://www.imgt.org/ligmdb/label)

References

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

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

See Also

sequences.functionality

Examples

data(summarytab)
junctionfr<-sequences.junctionFrame(data = summarytab$JUNCTION_frame)
barplot(as.numeric(junctionfr),xlab="",xlim=c(0,2),legend.text = colnames(junctionfr),
     col=c("orange","darkblue","gray"),xaxt="n",main="Junction frame usage",ylab="proportion")