getPopularMutationCount - Find Frequent Sequences’ Mutation Counts
getPopularMutationCount determines which sequences occur frequently
for each V gene and returns the mutation count of those sequences.
getPopularMutationCount(sample_db, germline_db, gene_min = 0.001, seq_min = 50, seq_p_of_max = 1/8, full_return = FALSE)
- A Change-O db data frame. See findNovelAlleles for a list of required columns.
- A named list of IMGT-gapped germline sequences.
- The portion of all unique sequences a gene must constitute to avoid exclusion.
- The number of copies of the V that must be present for to avoid exclusion.
- For each gene, fraction of the most common V sequence’s count that a sequence must meet to avoid exclusion.
- If true, will return all
sample_dbcolumns and will include sequences with mutation count < 1.
A data frame of genes that have a frequent sequence mutation count above 1.
data(sample_db, germline_ighv) getPopularMutationCount(sample_db, germline_ighv)
# A tibble: 1 × 2 V_GENE MUTATION_COUNT <chr> <int> 1 IGHV1-8 1
getMutatedPositions can be used to find which positions of a set of sequences are mutated.