setRegionBoundaries - Build a RegionDefinition object that includes CDR3 and FWR4.


setRegionBoundaries takes as input a junction length and an IMGT-numbered sequence and outputs a custom RegionDefinition object that includes the boundary definitions of CDR1-3 and FWR1-4 for that sequence. In contrast to the universal RegionDefinition object that end with FWR3, the returned definition is per-sequence due to variable junction lengths.


setRegionBoundaries(juncLength, sequenceImgt, regionDefinition = NULL)


junction length of the sequence.
IMGT-numbered sequence.
RegionDefinition type to calculate the region definition for. Can be one of IMGT_VDJ_BY_REGIONS or IMGT_VDJ, which are template definitions that include CDR1-3 and FWR1-4. Only these two regions include all CDR1-3 and FWR1-4 regions. If this argument is set to NULL, then an empty RegionDefinition will be returned.


A RegionDefinition object that includes CDR1-3 and FWR1-4 for the
sequenceImgt, juncLength, and regionDefinition specified.

For regionDefinition=IMGT_VDJ_BY_REGIONS, the returned RegionDefinition includes:

  • fwr1: Positions 1 to 78.
  • cdr1: Positions 79 to 114.
  • fwr2: Positions 115 to 165.
  • cdr2: Positions 166 to 195.
  • fwr3: Positions 196 to 312.
  • cdr3: Positions 313 to (313 + juncLength - 6) since the junction sequence includes (on the left) the last codon from FWR3 and (on the right) the first codon from FWR4.
  • fwr4: Positions (313 + juncLength - 6 + 1) to the end of the sequence.

For regionDefinition=IMGT_VDJ, the returned RegionDefinition includes:

  • fwr: Positions belonging to a FWR.
  • cdr: Positions belonging to a CDR.

In the case that the regionDefinition argument is not one of the extended regions (IMGT_VDJ_BY_REGIONS or IMGT_VDJ), the input regionDefinition is returned as is.


# Load and subset example data
data(ExampleDb, package = "alakazam")  
len <- ExampleDb$junction_length[1]
sequence <- ExampleDb$sequence_alignment[1]
region <- setRegionBoundaries(len, sequence, regionDefinition = IMGT_VDJ)

See also

See RegionDefinition for the return object. See IMGT_SCHEMES for a set of predefined RegionDefinition objects.