getPopularMutationCount - Find Frequent Sequences’ Mutation Counts

Description

getPopularMutationCount determines which sequences occur frequently for each V gene and returns the mutation count of those sequences.

Usage

getPopularMutationCount(sample_db, germline_db, gene_min = 0.001,
seq_min = 50, seq_p_of_max = 1/8, full_return = FALSE)

Arguments

sample_db
A Change-O db data frame. See findNovelAlleles for a list of required columns.
germline_db
A named list of IMGT-gapped germline sequences.
gene_min
The portion of all unique sequences a gene must constitute to avoid exclusion.
seq_min
The number of copies of the V that must be present for to avoid exclusion.
seq_p_of_max
For each gene, fraction of the most common V sequence’s count that a sequence must meet to avoid exclusion.
full_return
If true, will return all sample_db columns and will include sequences with mutation count < 1.

Value

A data frame of genes that have a frequent sequence mutation count above 1.

Examples

data(sample_db, germline_ighv)
getPopularMutationCount(sample_db, germline_ighv)
# A tibble: 1 × 2
   V_GENE MUTATION_COUNT
    <chr>          <int>
1 IGHV1-8              1

See also

getMutatedPositions can be used to find which positions of a set of sequences are mutated.