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.

Examples

getPopularMutationCount(AIRRDb, SampleGermlineIGHV)