A function to artificially create an IGHV reference set with framework1 (FWR1) primers (see Details).
artificialFRW1Germline(
germline_set,
mask_primer = TRUE,
trimm_primer = FALSE,
quite = FALSE
)A list with the input germline set allele and the trimmed/masked sequences.
A germline set distance matrix created by ighvDistance.
Logical (TRUE by default). If to mask with Ns the region of the primer from the germline sequence
Logical (FALSE by default). If to trim the region of the primer from the germline sequence. If TRUE then, mask_primer is ignored.
Logical (FALSE by default). Do you want to suppress informative messages
The FRW1 primers used in this function were taken from the BIOMED-2 protocol. For more information on the protocol and primer design go to: van Dongen, J., Langerak, A., Brüggemann, M. et al. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: Report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia 17, 2257–2317 (2003). https://doi.org/10.1038/sj.leu.2403202Van Dongen, J. J. M., et al. "Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936." Leukemia 17.12 (2003): 2257-2317.