extractVRegion: Extracts FWRs and CDRs from IMGT-gapped sequences

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Extracts FWRs and CDRs from IMGT-gapped sequences

Description

extractVRegion extracts the framework and complementarity determining regions of the V segment for IMGT-gapped immunoglobulin (Ig) nucleotide sequences according to the IMGT numbering scheme.

Usage

extractVRegion(sequences, region = c("fwr1", "cdr1", "fwr2", "cdr2", "fwr3"))

Arguments

sequences	character vector of IMGT-gapped nucleotide sequences.
region	string defining the region(s) of the V segment to extract. May be a single region or multiple regions (as a vector) from c("fwr1", "cdr1", "fwr2", "cdr2" ,"fwr3"). By default, all regions will be returned.

Value

If only one region is specified in the region argument, a character vector of the extracted sub-sequences will be returned. If multiple regions are specified, then a character matrix will be returned with columns corresponding to the specified regions and a row for each entry in sequences.

References

1. Lefranc M-P, et al. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol. 2003 27(1):55-77.

See Also

IMGT-gapped region boundaries are defined in IMGT_REGIONS.

Examples

# Assign example clone
clone <- subset(ExampleDb, clone_id == 3138)

# Get all regions
extractVRegion(clone$sequence_alignment)

# Get single region
extractVRegion(clone$sequence_alignment, "fwr1")

# Get all CDRs
extractVRegion(clone$sequence_alignment, c("cdr1", "cdr2"))

# Get all FWRs
extractVRegion(clone$sequence_alignment, c("fwr1", "fwr2", "fwr3"))

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.