| extractVRegion {alakazam} | R Documentation |
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.
extractVRegion(sequences, region = c("FWR1", "CDR1", "FWR2", "CDR2",
"FWR3"))
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
|
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.
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.
IMGT-gapped region boundaries are defined in IMGT_REGIONS.
# 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"))