sidier (version 2.2)

GetHaplo: Get sequences of unique haplotypes

Description

This function returns the subset of unique sequences composing a given alignment.

Usage

GetHaplo(inputFile = NA, align = NA, saveFile = T,
outname = "Haplotypes.txt", format = "fasta", seqsNames = NA)

Arguments

inputFile

the name of the alingment file in fasta format to be analysed.

align

the name of a sequence alignment stored in memory to be analysed. See "read.dna" in ape package for details about reading alignments.

saveFile

a logical; if TRUE (default), function output is saved as a text file

outname

if "saveFile" is set to TRUE (default), contains the name of the output file ("Haplotypes.txt" by default).

format

format of the DNA sequences to be saved: "interleaved", "sequential", or "fasta" (default). See "write.dna" in ape package for details.

seqsNames

names for each DNA sequence saved: Three choices are possible: if n unique sequences are found, "Inf.Hap" assign names from H1 to Hn (according to input order). The second option is to define a vector containing n names. By default, input sequence names

Value

• A file containing unique sequences from the input file.

Details

If two equal sequences are not identically aligned, they will be considered as different haplotypes. To avoid misleading results in uncertain alignments it is recommended to use as input the original unaligned sequences, including gaps after the last nucleotide of short sequences to make all sequence lengths equal.

Examples

#generating an alignment file:
cat(">Population1_sequence1",
"TTATAAAATCTA----TAGC",
">Population1_sequence2",
"TAAT----TCTA----TAAC",
">Population1_sequence3",
"TTATAAAAATTA----TAGC",
">Population1_sequence4",
"TAAT----TCTA----TAAC",
">Population2_sequence1",
"TTAT----TCGAGGGGTAGC",
">Population2_sequence2",
"TAAT----TCTA----TAAC",
">Population2_sequence3",
"TTATAAAA--------TAGC",
">Population2_sequence4",
"TTAT----TCGAGGGGTAGC",
">Population3_sequence1",
"TTAT----TCGA----TAGC",
">Population3_sequence2",
"TTAT----TCGA----TAGC",
">Population3_sequence3",
"TTAT----TCGA----TAGC",
">Population3_sequence4",
"TTAT----TCGA----TAGC",
     file = "ex2.fas", sep = "")

# Getting unique haplotypes reading the alignment from a file and setting
#haplotype names:
	GetHaplo(inputFile="ex2.fas",outname="ex2_unique.fas",seqsNames=
c("HaploK001","HaploK002","HaploS001","HaploR001","HaploR002","HaploR003"))
# Reading the alignment from an object and using original sequence names:
    library(ape)
    example2 <- read.dna("ex2.fas", format = "fasta")
	GetHaplo(align=example2,outname="Haplotypes_DefaultNames.txt")
# Reading the alignment from an object and using haplotype names:
	GetHaplo(align=example2,outname="Haplotypes_sequentialNames.txt",
seqsNames="Inf.Hap")