flag_position: 'flag_position'

In ludwigHoon/minSNPs: Resolution-Optimised SNPs Searcher

flag_position

Description

flag_position is used to find out positions that will be ignored in calculation (either not A,C,G,T or '-'), can be case sensitive or insensitive.

Usage

flag_position(
  pro_seqc,
  dash_ignore = TRUE,
  accepted_char = c("A", "C", "T", "G"),
  ignore_case = TRUE,
  remove_invariant = FALSE,
  biallelic_only = FALSE,
  bp = SerialParam()
)

Arguments

pro_seqc	Sequences after processed, i.e. all with the same length
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 a list of positions that need to be ignored.

ludwigHoon/minSNPs documentation built on March 25, 2024, 11:54 a.m.