sidier (version 2.0)

FindHaplo: Find equal haplotypes

Description

This function assigns the same name to equal haplotypes in a sequence alignment.

Usage

FindHaplo(inputFile = NA, align = NA, saveFile = T,
outname = "FindHaplo.txt")

Arguments

inputFile

the name of a sequence alignment 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 ("FindHaplo.txt" by default).

Value

• A two columns matrix containing the original sequence name and the haplotype name assigned to each sequence in the input alignment.

See Also

HapPerPop

Examples

#generating an alignment file:
cat(">Population1_sequence1",
"TTATAGGTAGCTTCGATATTG",
">Population2_sequence1",
"TTA---GTAGCTTCGAAATTG",
">Population3_sequence1",
"TTA---GTA---TCG---TAG",
">Population4_sequence1",
"TTATAGGTA---TCG---TTG",
">Population5_sequence1",
"TTA------------AAATTG",
file = "ex1.fas", sep = "")

	 # Reading the alignment directly from file:
	 FindHaplo(input="ex1.fas") 

	 # Reading the alignment from an object:
library(ape)
example1<-read.dna(file="ex1.fas",format="fasta")
FindHaplo(align=example1)