sidier (version 4.1.0)

FilterHaplo: Filter haplotypes by occurrence

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.

Examples

# NOT RUN {
# 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)
# }