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

In shazam: Immunoglobulin Somatic Hypermutation Analysis

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 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.

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.

See Also

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

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)

shazam documentation built on Oct. 3, 2023, 1:06 a.m.