Description Usage Arguments Details Value Author(s) References See Also Examples
This function gives information about the proportion of in-frame and out-of-frame sequences.
1 | sequences.junctionFrame(data = NULL, relativeValues=TRUE, ...)
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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) |
... |
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)
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.
Julia Bischof
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
1 2 3 4 | 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")
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