Conducts a suite of data summaries. Summarizes missing data and
homozygosity by individual and locus, and looks for duplicate genotypes
(see dupGenotypes). For sequence data, identifies low
frequency substitutions (see lowFreqSubs), and computes
sequence likelihoods (see sequenceLikelihoods).
summarizeAll(g, write.files = FALSE, label = NULL, ...)logical determining whether to write .csv files of summaries
optional label for output folder and prefix for files.
optional arguments to pass on to summary functions.
If write.files = TRUE, files are written for by-sample and
by-locus summaries, and duplicate genotypes if any are found. If
sequences are present, files are written identifying low frequency
substitutions and sequence likelihoods.
The return value is a list with the following elements:
data.frame of by-sample summaries
by.locusdata.frame of by-locus summaries
dup.dfdata.frame identifying potential duplicates
by.seqlist of low frequency substitutions and haplotype likelihoods for each gene
summarizeInds, summarizeLoci,
dupGenotypes, lowFreqSubs,
sequenceLikelihoods