reassignAlleles - Correct allele calls based on a personalized genotype
reassignAlleles uses a subject-specific genotype to correct
correct preliminary allele assignments of a set of sequences derived
from a single subject.
reassignAlleles(clip_db, genotype_db, method = "hamming", path = NA, keep_gene = TRUE)
data.framecontaining V allele calls from a single subject under
"V_CALL"and the sample IMGT-gapped V(D)J sequences under
- a vector of named nucleotide germline sequences
matching the calls detailed in
allele_callsand personalized to the subject
- the method to be used when realigning sequences to the genotype_db sequences. Currently only “hammming” (for Hamming distance) is implemented.
- directory containing the tool used in the realignment method, if needed. Hamming distance does not require a path to a tool.
- logical indicating if gene assignments should be maintained when possible. Increases speed by minimizing required number of alignments. Currently only “TRUE” is implemented.
data.frame corresponding to
and containing the best allele call from among the sequences
In order to save time, initial gene assignments are preserved and
the allele calls are chosen from among those provided in
based on a simple alignment to the sample sequence.
# Load example data data(germline_ighv) data(sample_db) data(genotype) data(novel_df) # Extract the database sequences that correspond to the genotype genotype_seqs = genotypeFasta(genotype, germline_ighv, novel_df) # Use the personlized genotype to determine corrected allele assignments V_CALL_GENOTYPED = reassignAlleles(sample_db, genotype_seqs) sample_db = cbind(sample_db, V_CALL_GENOTYPED)