inst/doc/summaries.R

In strataG: Summaries and Population Structure Analyses of Genetic Data

## ----echo = FALSE, message = FALSE--------------------------------------------
options(digits = 2)
library(strataG)

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data(msats.g)
msats <- stratify(msats.g, "broad")
msats <- msats[, getLociNames(msats)[1:4], ]

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numAlleles(msats)

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numMissing(msats)

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numMissing(msats, prop = TRUE)

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allelicRichness(msats)

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# observed
heterozygosity(msats, type = "observed")

# expected
heterozygosity(msats, type = "expected")

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propUniqueAlleles(msats)

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theta(msats)

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summarizeLoci(msats)
summarizeLoci(msats, by.strata = TRUE)

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alleleFreqs(msats)
alleleFreqs(msats, by.strata = TRUE)

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# Find samples that share alleles at 2/3rds of the loci
dupGenotypes(msats, num.shared = 0.66)

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library(ape)
data(dolph.seqs)
seq.smry <- summarizeSeqs(as.DNAbin(dolph.seqs))
head(seq.smry)

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bf <- baseFreqs(as.DNAbin(dolph.seqs))

# nucleotide frequencies by site
bf$site.freq[, 1:15]

# overall nucleotide frequencies
bf$base.freqs

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lowFreqSubs(as.DNAbin(dolph.seqs), min.freq = 2)

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data(dolph.haps)
sequenceLikelihoods(as.DNAbin(dolph.haps))