strataG (version 2.4.905)

summarizeAll: Summarize Genotypes and Sequences

Description

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).

Usage

summarizeAll(g, write.files = FALSE, label = NULL, ...)

Arguments

g

a '>gtypes object.

write.files

logical determining whether to write .csv files of summaries

label

optional label for output folder and prefix for files.

...

optional arguments to pass on to summary functions.

Value

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:

by.sample

data.frame of by-sample summaries

by.locus

data.frame of by-locus summaries

dup.df

data.frame identifying potential duplicates

by.seq

list of low frequency substitutions and haplotype likelihoods for each gene

See Also

summarizeInds, summarizeLoci, dupGenotypes, lowFreqSubs, sequenceLikelihoods