This repo contains R functions to estimate error rates; to generate the a list of white loci and population maps to run the populations program of Stacks; to perform a PCoA; and, to estimate the distance between individuals of the same population. The scripts assume than several datasets will be compared (e.g. the several outputs of assembling the data with different parameters).

The R functions to estimate the loci, allele and SNP error rates are:

• LociAllele_error.R, which uses a tsv matrix of alleles and loci (formated as the output of export_sql from Stacks but keeping only the columns CatalogID Consensus SNPs Sample1 Sample1_r Sample2 ...) to convert it to genlight object to estimate loci and allele error rates between replicate pairs. The function produces a dataframe with the following columns for each replicate pair:

• "nloci" = total number of loci in the dataset

• "nMissLoc" = number of missing loci for both samples of a replicate pair

• "MissTotProp", = nMissLoc/nloci

• "shareMissLoc" = number of loci that are lost in both samples of replicate pair

• "loci.mismatches" = number of loci that failed in the sample or replicate, but not in both

• "unshareMissLoc" = loci.mismatches/nMissLoc

• "loci.error.rate" = loci.mismatches/nloci

• "n.loci.woNA" = number of loci that were NOT missing in both samples or a replicate pair

• "allele.mismatches" = number of alleles that mismatch between samples of a replicate pair

• "allele.error.rate" allele.mismatches/n.loci.woNA

and

• SNPs_error.R that uses a genlight object of SNPs, (obtained by e.g. transforming a plink.raw to genlight object) to estimate SNP error rates.

The function PairsDiff.R wraps up LociAllele_error. and SNPs_error.R to estimate loci, allele and SNP error rates and visualize the Matrix of SNPs as a plot.

• whitePopMap.R creates a list of the samples present in a desired df (e.g. a subsection or of the tsv output of explort_sql) and writes a file that can be read by Stacks as a Population Map of desired samples to analyse with the populations program

• whiteRADlist.R creates a list of the CatalogID loci present in a desired matrix and write a file that can be read by Stacks as whitelist of desired loci to perform analyses with the populations program.

• dist.pop.R estimate distance between individuals of the same population
• PCoA_pop.r performs a PCoA.