artificialFRW1Germline: FWR1 artificial dataset generator

In piglet: Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes

FWR1 artificial dataset generator

Description

A function to artificially create an IGHV reference set with framework1 (FWR1) primers (see Details).

Usage

artificialFRW1Germline(
  germline_set,
  mask_primer = TRUE,
  trimm_primer = FALSE,
  quite = FALSE
)

Arguments

germline_set	A germline set distance matrix created by ighvDistance.
mask_primer	Logical (TRUE by default). If to mask with Ns the region of the primer from the germline sequence
trimm_primer	Logical (FALSE by default). If to trim the region of the primer from the germline sequence. If TRUE then, mask_primer is ignored.
quite	Logical (FALSE by default). Do you want to suppress informative messages

Details

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.

Value

A list with the input germline set allele and the trimmed/masked sequences.

piglet documentation built on April 12, 2025, 1:27 a.m.