rm.connections {RMThreshold} | R Documentation |
Create ordered list of largest matrix elements
Description
The function creates a data frame which is sorted according to the (absolute) magnitude of the matrix elements.
Usage
rm.connections(mat, nr.list = 30, abs.val = TRUE, fn = NULL)
Arguments
mat |
Input matrix. |
nr.list |
Number of matrix elements to show. |
abs.val |
Logical variable determining if absolute values should be used for sorting. |
fn |
A file name. If not |
Details
This function can for instance be useful if pairs of samples with the largest correlation/mutual information are to be identified. By default, the matrix elements are sorted according to their absolute values. The list will not be saved if no filename is invoked, otherwise it will be saved to a tab-separated text file.
Value
A data frame containing the values of the largest nr.list
matrix elements, together with the respective row- and column numbers. If present, the referring row- and column names are also included.
Author(s)
Uwe Menzel <uwemenzel@gmail.com>
Examples
set.seed(777)
random.mat <- create.rand.mat(size = 1000, distrib = "norm")$rand.matr
dim(random.mat)
## After identification of a proper threshold:
cleaned.matrix <- rm.denoise.mat(random.mat, threshold = 3.2, keep.diag = TRUE)
cl2.matrix = rm.discard.zeros(cleaned.matrix)
df = rm.connections(cl2.matrix)