pcadapt (version 1.0)

outlier: Analysis of the computed p-values

Description

outlier returns an object x containing a list of indices (x$outliers) corresponding to the SNPs ranked by the chosen p-values associated with K-th principal component or obtained with the meta-analysis (x$pvalues), as well as a list of false discovery rates computed for different thresholds (which are set in the built-in function fdrList) in the case of a simulation.

Usage

outlier(y, K = NULL, threshold = 0.1, list_selection = NULL)

Arguments

y

an object of class pcadapt generated with pcadapt.

K

an integer specifying the principal component the user is interested in. Default value set to 1. NB : this field can be left empty in the meta-analysis case.

threshold

a real value between 0 and 1 indicating the proportion of false discoveries to be tolerated.

list_selection

a vector of indices containing the list of all the SNPs under selection in the case of a simulation. When this argument is provided, a list of false discovery rates is calculated for different thresholds. Default value is set to NULL.

Examples

x <- read4pcadapt("geno3pops",option="example")
y <- pcadapt(x,K=3)
outlier(y,K=1)