process_allele {minSNPs}

process_allele

Description

process_allele is used to returned the processed allelic profiles, by removing the allele profile with duplicate name and length different from most. 1st allele profile with the duplicated name is returned, the longer length is taken as normal should there be 2 modes.

Usage

process_allele(
  seqc,
  bp = BiocParallel::SerialParam(),
  check_length = TRUE,
  check_bases = TRUE,
  dash_ignore = TRUE,
  accepted_char = c("A", "C", "T", "G"),
  ignore_case = TRUE,
  remove_invariant = FALSE,
  biallelic_only = FALSE
)

Arguments

seqc

a list containing list of nucleotides. To keep it simple, use provided read_fasta to import the fasta file.

bp

is the biocparallel backend, default to serialParam, most likely sufficient in most scenario

check_length

Check the length of each sample in the matrix, default to TRUE

check_bases

Check the bases of each sample in the matrix, default to TRUE

dash_ignore

whether to treat '-' as another type

accepted_char

character to accept, default to c("A", "C", "T", "G")

ignore_case

whether to be case insensitive, default to TRUE

remove_invariant

whether to remove invariant positions, default to FALSE

biallelic_only

whether to remove positions with more than 2 alleles, default to FALSE

Value

Will return the processed allelic profiles.