export.groups: Export the ipcaps result to a text file

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

Description

Export clustering result of ipcaps to text file called 'groups.txt'.

Usage

export.groups(result.dir, silence.mode = FALSE)

Arguments

result.dir	A result directory as the $output object returned from the ipcaps function.
silence.mode	To enable or disable silence mode. If silence mode is enabled, the fuction is processed without printing any message on the screen, and it is slightly faster. Default = TRUE.

Details

After running, this function exports the file called 'groups.txt' to the same result directory. If 'groups.txt' already exists in the result directory, the exported file is changed to 'groups1.txt', 'groups2.txt', 'groups3.txt', ..., accordingly.

Value

A data frame of exported data containing 4 columns; group, node, label, row.number, as described below for more details:

• group represents group membership of ipcaps result.

• node represents node numbers of ipcaps result.

• label represents labels of rows in orginal input data.

• row.number represents row numbers of orginal input data.

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 export the ipcaps result to a text file
exported.data <- export.groups(my.cluster$output.dir)
print(dim(exported.data))
head(exported.data)

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