pcadapt objects

Description

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

Usage

1
create.pcadapt(output.filename, K, method, data.type, min.maf)

Arguments

output.filename

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

K

an integer specifying the number of principal components to retain.

method

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

data.type

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

min.maf

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