R: Extracts FWRs and CDRs from IMGT-gapped sequences

extractVRegion {alakazam} | R Documentation

## 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 == 3138)

    # 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"))

[Package alakazam version 0.3.0 Index]