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I want to use a gene alignment of 185 individuals to calculate the pairwise Fst stats for them.</p>
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My initial plan was:</p>
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Import the alignment, transform to DNAbin, transform to genind, the use that file to calculate the pairwise Fst.</p>
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I have some questions:</p>
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To use the function 'pairwise.fst' from the package pegas, I need to have diploid genind object. However my genind file is haploid. How can I alter that? Do I need to use the "df2genind" function? If so, what is the proper way to convert the alignment into
a data frame?</p>
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How can I alter the populations for each individual? Do I need an additional object/dataframe with the population info? And how can I perform such action? Through the 'setPop' function?</p>
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Please see the script as it follows and my alignment attached.</p>
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Thank you for your time</p>
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Cheers</p>
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JP</p>
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### Attempt to use 'adegenet' to calculate Fst of sanger alignments ###</p>
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require (adegenet)</p>
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require (pegas)</p>
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require (hierfstat)</p>
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#Set working directory</p>
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setwd("~/Documents/Lab/PhD/steatogenys/fst/")</p>
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#Import/read fasta alignment using fasta2DNAbin function</p>
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#Will read the alignment and transform into DNAbin, which is used</p>
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#To calculate Fst</p>
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# The important thing is that the alignment (dna) file has to be transformed into DNAbin file</p>
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#Note alignment has to be same size, and clean, for each seq.</p>
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ali <- fasta2DNAbin("atpcleanFULL_name.fas", chunk = 10)</p>
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#chuck = how many seqs processed at a time</p>
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#Transform DNAbin file in a data.matrix</p>
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myali <- as.matrix(ali)</p>
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#transform DNAbin object into genind object, calculates alleles, etc.</p>
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# CHECK ARGUMENTS, % of polymorphism, pops, etc.</p>
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obj <- DNAbin2genind(myali)</p>
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#Calculate pairwise Fst NOT WORKING</p>
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matFst <- pairwise.fst(obj)</p>
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------------</p>
<p style="margin: 0px; line-height: normal; font-family: 'Helvetica Neue'; color: rgb(51, 51, 51);">
João Pedro Fontenelle</p>
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Dept. of Biological Sciences</p>
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Dept. of Physical and Environmental Sciences</p>
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University of Toronto Scarborough</p>
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Office S552</p>
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1265 Military Trail</p>
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M1C 1A4</p>
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Toronto, ON, Canada</p>
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