FilterHaplo: Filter haplotypes by occurrence

In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

Description

Provides a subset of a original alignment composed only of haplotypes showing the range of occurrences provided

Usage

FilterHaplo(inputFile=NA, align=NA, Nmin=0, Nmax=NULL,
 saveFile=FALSE, outname="FilterHaplo.txt")

Arguments

inputFile	the name of a sequence alignment file in fasta format to be analysed. Alternatively you can provide the name of a "DNAbin" class alignment stored in memory using the "align" option.
align	the name of the "DNAbin" alignment to be analysed. See "?read.dna" in the ape package for details about reading alignments. Alternatively you can provide the name of the file containing the alignment in fasta format using the "inputFile" option.
Nmin	Minimum occurrence of an haplotype to be included in the subset
Nmax	Maximum occurrence of an haplotype to be included in the subset
saveFile	a logical; if TRUE (default), function output is saved as a text file in fasta format
outname	if "saveFile" is set to TRUE (default), contains the name of the output file.

Author(s)

A. J. Muñoz-Pajares

Examples

# cat(">Population1_sequence1",
# "TTATAAAATCTA----TAGC",
# ">Population1_sequence2",
# "TAAT----TCTA----TAAC",
# ">Population1_sequence3",
# "TTATAAAAATTA----TAGC",
# ">Population1_sequence4",
# "TAAT----TCTA----TAAC",
# ">Population2_sequence1",
# "TTAT----TCGA----TAGC",
# ">Population2_sequence2",
# "TTAT----TCGA----TAGC",
# ">Population2_sequence3",
# "TTAT----TCGA----TAGC",
# ">Population2_sequence4",
# "TTAT----TCGA----TAGC",
# ">Population3_sequence1",
# "TTAT----TCGAGGGGTAGC",
# ">Population3_sequence2",
# "TAAT----TCTA----TAAC",
# ">Population3_sequence3",
# "TTATAAAA--------TAGC",
# ">Population3_sequence4",
# "TTAT----TCGAGGGGTAGC",
#      file = "ex2.fas", sep = "\n")
# library(ape)
# example<-read.dna(file="ex2.fas",format="fasta")
# 
# # Exclude unique haplotypes
# FilterHaplo(align=example,Nmin=2)
# 
# # Include only unique haplotypes
# FilterHaplo(align=example,Nmax=1)
# 
# # Filter haplotypes appearing between 2 and 4 times
# FilterHaplo(align=example,Nmax=4,Nmin=2)

sidier documentation built on June 25, 2021, 5:10 p.m.