sequences.getAnyFunctionality: Filter for productive or unproductive sequences

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description

Filter IMGT/HighV-QUEST output files for productive or unproductive sequences.

sequences.getProductives filters only productive sequences

sequences.getUnproductives filters only unproductive sequences

sequences.getAnyFunctionality filters all sequences with any functionality information (productive or unproductive)

Usage

sequences.getAnyFunctionality(data = NULL)

sequences.getProductives(data = NULL)

sequences.getUnproductives(data = NULL)

Arguments

data	IMGT/HighV-QUEST output file with functionality information, e.g. 1_Summary().txt, 3_Nt-sequences.txt, ...

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 with the same columns like the input, but filtered for only productive or unproductive sequences or sequences having any functionality information.

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.getAnyFunctionality, sequences.getProductives, sequences.getUnproductives,

sequences.functionality, sequences.getAnyJunctionFrame, sequences.getInFrames,

sequences.getOutOfFrames

Examples

data(summarytab)
ProductiveSequences<-sequences.getProductives(summarytab)
UnroductiveSequences<-sequences.getUnproductives(summarytab)
AnyFunctSequences<-sequences.getAnyFunctionality(summarytab)

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