R: Find mutation counts for frequency sequences

getPopularMutationCount {tigger} | R Documentation

## Find mutation counts for frequency sequences

### Description

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

### Usage

    getPopularMutationCount(
      data,
      germline_db,
      v_call = "v_call",
      seq = "sequence_alignment",
      gene_min = 0.001,
      seq_min = 50,
      seq_p_of_max = 1/8,
      full_return = FALSE
    )

### Arguments

`data` | `data.frame` in the Change-O format. See findNovelAlleles for a list of required columns.
`germline_db` | named list of IMGT-gapped germline sequences.
`v_call` | name of the column in `data` with V allele calls. Default is `v_call`.
`seq` | name of the column in `data` with the aligned, IMGT-numbered, V(D)J nucleotide sequence. Default is `sequence_alignment`.
`gene_min` | portion of all unique sequences a gene must constitute to avoid exclusion.
`seq_min` | number of copies of the V that must be present for to avoid exclusion.
`seq_p_of_max` | ror each gene, the fraction of the most common V sequence count that a sequence must meet to avoid exclusion.
`full_return` | if `TRUE`, will return all `data` columns and will include sequences with mutation count < 1.

### Value

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

### See Also

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

### Examples

    getPopularMutationCount(AIRRDb, SampleGermlineIGHV)

[Package tigger version 1.0.0 Index]