clustering: (Internal function) Perform the clustering process of IPCAPS2

In kridsadakorn/ipcaps2: Iterative Pruning to Capture Population Structure version 2

(Internal function) Perform the clustering process of IPCAPS2

Description

(Internal function) Perform the clustering process of IPCAPS2

Usage

clustering(
  dataframe,
  node = 1,
  result.dir,
  threshold,
  min.fst,
  method = "mix",
  min.in.group = 20,
  datatype = "snp",
  nonlinear = FALSE,
  no.rep = 5,
  cutoff.confident = 0.5
)

Arguments

dataframe	A data frame containing raw.data (matrix or data frame), label (vector), and index (vector). raw.data represents a matrix of subset of input data. label represents a vector of labels for all rows of raw.data. index represents a vector of indexes that are selected from the original input data.
node	An integer representing the current node number which is being analyzed.
result.dir	An output directory
threshold	A threshold or a cutoff to stop the IPCAPS2 process. Also see ipcaps2 (the parameter threshold).
min.fst	A number represents a cutoff for mininum Fst value.
method	A clustering method selected from the ipcaps2 function. See ipcaps2 for available methods.
min.in.group	A integer represents a minimum number of group members.
datatype	To specify whether the input data are 'snp' or other type. Defalut = 'snp'.
nonlinear	(Unimplemented) To specify whether linear or non-linear method is used for IPCAPS2 analysis. If TRUE, non-linear method is used, otherwise linear method is used. Default = FALSE.
no.rep	To specify a number of time to replicate the internal clustering. Default = 5,
cutoff.confident	To specify a cutoff for confident values. Default = 0.5.

Value

A list containing status, node, and new.index as explained below:

• $status is either 0 representing that the criterion is not met, or 1 representing that the criterion is met.

• $node is an integer representing the current node number which is being analyzed.

• $new.index is a list of vectors containing a subset of indexes split from dataframe$index according to a clustering result.

kridsadakorn/ipcaps2 documentation built on June 11, 2022, 8:35 p.m.