tigger (version 1.1.0)

getPopularMutationCount: 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
)

Value

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

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.

See Also

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

Examples

getPopularMutationCount(AIRRDb, SampleGermlineIGHV)