callNCW {ccml} | R Documentation |
Calculate normalized consensus weight(NCW) matrix based on permutation.
Description
Calculate normalized consensus weight(NCW) matrix based on permutation.
Usage
callNCW(
title = "",
label,
nperm = 10,
ncore = 1,
seedn = 100,
stability = TRUE,
plot = NULL
)
Arguments
title |
A character value for output directory. Directory is created only if not existed. This title can be an abosulte or relative path. |
label |
A matrix or data frame of input labels, columns=different clustering results and rows are samples. |
nperm |
A integer value of the permutation numbers, or nperm=10(default), which means |
ncore |
A integer value of cores to use, or ncore=1 (default). It's the input core numbers for the parallel computation in this package |
seedn |
A numerical value to set the start random seed for reproducible results, or seedn=100 (default). For every 1000 iteration, the seed will +1 to get repeat results. |
stability |
A logical value. Should estimate the stability of normalized consensus weight based on permutation numbers (default stability=TRUE), or not? |
plot |
character value. NULL(default) - print to screen, 'pdf', 'png', 'pngBMP' for bitmap png, helpful for large datasets, or 'pdf'. Input for |
Value
A matrix of normalized consensus weights.
Examples
# load data
data(example_data)
label=example_data
# if plot is not NULL, results will be saved in "result_output" directory
title="result_output"
# run ncw
ncw<-callNCW(title=title,label=label,stability=TRUE,nperm=4,ncore=1)