setRegionBoundaries - Build a RegionDefinition object that includes CDR3 and FWR4.
Description¶
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.
Usage¶
setRegionBoundaries(juncLength, sequenceImgt, regionDefinition = NULL)
Arguments¶
- juncLength
- junction length of the sequence.
- sequenceImgt
- IMGT-numbered sequence.
- regionDefinition
RegionDefinition
type to calculate the region definition for. Can be one ofIMGT_VDJ_BY_REGIONS
orIMGT_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 toNULL
, then an emptyRegionDefinition
will be returned.
Value¶
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.
Examples¶
# 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.