create.pcadapt

a character string indicating which outputs from PCAdapt
fast should be processed.

output.filename

an integer specifying the number of principal components to retain.

a character string specifying the method to be used to compute
the p-values. Four statistics are currently available, <code>"mahalanobis"</code>,
<code>"communality"</code>, and <code>"componentwise"</code>.

method

a character string specifying the type of data being read, either
a <code>genotype</code> matrix (<code>data.type="genotype"</code>), or a matrix of allele
frequencies (<code>data.type="pool"</code>).

data.type

a value between <code>0</code> and <code>0.45</code> specifying the threshold
of minor allele frequencies above which p-values are computed.

min.maf


<code>create.pcadapt</code> loads the numerical quantities needed to compute the test
statistics, and stores them in an object of class <code>pcadapt</code>.


internal

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>.

create.pcadapt: pcadapt objects

Description

Usage

Arguments