getPairGMMEdges: Performs pair-wise Gaussian Mixture Models (GMM) on a pair of...

In SystemsGenetics/KINC.R: Provides additional functions for network files created using KINC.

Description

Performs pair-wise Gaussian Mixture Models (GMM) on a pair of genes

Usage

getPairGMMEdges(
  source,
  target,
  ematrix,
  minc = 30,
  method = "spearman",
  th = 0.5,
  plot = FALSE,
  iterations = 5
)

Arguments

source	The name of the source gene.
target	The name of the target gene.
ematrix	The expression matrix data frame.
minc	The minimum number of samples that must be present to identify a cluster. Default = 30.
method	The correlation method to perform (see the cor function for valid options)
th	The similarity value threshold. Any correlation value greater than or equal to the absolute value of this number is kept as an edge. Derfault = 0.5.
plot	Boolean indicating if the Rmixmod clusters scatterplot should be drawn. Default = FALSE
iterations	The number of times to execute the GMM models. The model with the fewest clusters from all the iterations will be used.

Value

Returns a data frame of edges in the same format as the network returned by the loadNetwork function.

SystemsGenetics/KINC.R documentation built on Nov. 10, 2021, 9:22 p.m.