get.node.info: Get the information for specified node

In kridsadakorn/ipcaps.bioc: Iterative Pruning to Capture Population Structure

Description

Obtain the information for specified node from the output list of ipcaps.

Usage

get.node.info(cluster.obj, node)

Arguments

cluster.obj	A list returned from the ipcaps function.
node	An integer representing a node number to enquire information as shown in the HTML output files.

Value

The return value is NULL if node's information does not exist or a list containing. PCs, eigen.fit, index, and label as explained below:

• $PCs is a matrix of pricipal components of this node.

• $eigen.fit is a number represeting the EigenFit value of this node.

• $index is a vector of row number (individuals) of raw.data (input data).

• $label is the vector of labels of all individuals that belongs to this node.

Examples

# Importantly, bed file, bim file, and fam file are required
# Use the example files embedded in the package

BED.file <- system.file('extdata',
                        'ipcaps_example.bed',
                        package = 'IPCAPS.BIOC')

LABEL.file <- system.file('extdata',
                          'ipcaps_example_individuals.txt.gz',
                          package = 'IPCAPS.BIOC')

my.cluster <- ipcaps(bed = BED.file,
                     label.file = LABEL.file,
                     lab.col = 2,
                     out = tempdir(),
                     max.thread = 1,
                     seed = 1234)

#Here, to obtain the information of specified node, for example, node 3
node.info <- get.node.info(my.cluster,3)

kridsadakorn/ipcaps.bioc documentation built on Jan. 22, 2020, 11:18 p.m.