sequences.getAnyJunctionFrame: Filter for in-frame or out-of-frame sequences

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description

Filter IMGT/HighV-QUEST output files for in-frame or out-of-frame sequences.

sequences.getInFrames filters only in-frame sequences

sequences.getOutOfFrames filters only out-of-frame sequences

sequences.getAnyJunctionFrame filters all sequences with any junction frame information (in-frame or out-of-frame)

Usage

sequences.getAnyJunctionFrame(data = NULL)

sequences.getInFrames(data = NULL)

sequences.getOutOfFrames(data = NULL)

Arguments

data	IMGT/HighV-QUEST output file with junction frame information, e.g. 1_Summary().txt, ...

Value

Output is a data frame with the same columns like the input, but filtered for only in-frame or out-of-frame sequences or sequences having any junction frame information.

Author(s)

Julia Bischof

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.getAnyJunctionFrame, sequences.getInFrames, sequences.getOutOfFrames,

sequences.junctionFrame, sequences.getAnyFunctionality, sequences.getProductives,

sequences.getUnproductives

Examples

data(summarytab)
InFrameSequences<-sequences.getInFrames(summarytab)
OutOfFrameSequences<-sequences.getOutOfFrames(summarytab)
AnyJunctionFrSequences<-sequences.getAnyJunctionFrame(summarytab)

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