seqs2hap: Generate Hap Results from Seqs

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

Generate Hap Results from Seqs

Description

generate hapResults from aligned and trimed sequences

Usage

seqs2hap(
  seqs,
  Ref = names(seqs)[1],
  hetero_remove = TRUE,
  na_drop = TRUE,
  maxGapsPerSeq = 0.25,
  hapPrefix = "H",
  pad = 3,
  chrName = "Chr0",
  ...
)

trimSeqs(seqs,
         minFlankFraction = 0.1)

Arguments

seqs	object of DNAStringSet or DNAMultipleAlignment class
Ref	the name of reference sequences. Default as the name of the first sequence
hetero_remove	whether remove accessions contains hybrid site or not. Default as TRUE
na_drop	whether drop sequeces contain "N" Default as TRUE.
maxGapsPerSeq	value in ⁠[0, 1]⁠ that indicates the maximum fraction of gaps allowed in each seq after alignment (default as 0.25). Seqs with gap percent exceed that will be dropped
hapPrefix	prefix of hap names. Default as "H"
pad	The number length in haplotype names should be extend to.
chrName	the Name should be used for haplotype
...	Parameters not used.
minFlankFraction	A value in ⁠[0, 1]⁠ that indicates the minimum fraction needed to call a gap in the consensus string (default as 0.1).

Value

object of hapResult class

Examples

data("geneHapR_test")
seqs
seqs <- trimSeqs(seqs,
         minFlankFraction = 0.1)
seqs
hapResult <- seqs2hap(seqs,
                      Ref = names(seqs)[1],
                      hetero_remove = TRUE, na_drop = TRUE,
                      maxGapsPerSeq = 0.25,
                      hapPrefix = "H")

geneHapR documentation built on May 29, 2024, 11:59 a.m.