View source: R/RegionsExtend.R
setRegionBoundaries | R Documentation |
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)
juncLength |
junction length of the sequence. |
sequenceImgt |
IMGT-numbered sequence. |
regionDefinition |
|
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.
See RegionDefinition for the return object.
See IMGT_SCHEMES for a set of predefined RegionDefinition
objects.
# 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)
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