alakazam (version 0.2.2)

extractVRegion: 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.

Other sequence annotation functions: getSegment

Examples

# Load example data
file <- system.file("extdata", "ExampleDb.gz", package="alakazam")
df <- readChangeoDb(file)
clone <- subset(df, CLONE == 164)

# Get all regions
extractVRegion(clone$SEQUENCE_IMGT)

# Get single region
extractVRegion(clone$SEQUENCE_IMGT, "FWR1")

# Get all CDRs
extractVRegion(clone$SEQUENCE_IMGT, c("CDR1", "CDR2"))

# Get all FWRs
extractVRegion(clone$SEQUENCE_IMGT, c("FWR1", "FWR2", "FWR3"))