read.pcadapt

a character string specifying the name of the file to be
converted if <code>local.env = FALSE</code>. If <code>local.env = TRUE</code>, <code>input.filename</code> refers
to the genotype matrix in the local environment.

input.filename

a character string specifying the type of data to be converted to the
<code>pcadapt</code> format. Supported formats are: <code>ped</code>, <code>vcf</code>, <code>lfmm</code>.

type

a logical value indicating whether the input has to be read from the local
environment or from the working directory.

local.env

an integer specifying the ploidy of the individuals.

ploidy

a vector specifying the number of individuals for each pool.

pop.sizes

a character string specifying the type of allele separator used in VCF files. Set to "/" by default, but can
be switched to "|" otherwise.

allele.sep

an integer specifying the number of markers to be processed in the mean time.

blocksize


<code>read.pcadapt</code> converts <code>.vcf</code> and <code>.ped</code> files to an appropriate
type of file readable by <code>pcadapt</code>. You may find the converted file in the
current directory.


Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis. Implements the method described in (Luu, 2016)
<DOI:10.1111/1755-0998.12592>.

read.pcadapt: File Converter

Description

Usage

Arguments