unsignedAdjacency: Calculation of unsigned adjacency

In WGCNA: Weighted Correlation Network Analysis

Calculation of unsigned adjacency

Description

Calculation of the unsigned network adjacency from expression data. The restricted set of parameters for this function should allow a faster and less memory-hungry calculation.

Usage

unsignedAdjacency(
  datExpr, 
  datExpr2 = NULL, 
  power = 6, 
  corFnc = "cor", corOptions = "use = 'p'")

Arguments

datExpr	expression data. A data frame in which columns are genes and rows ar samples. Missing values are ignored.
datExpr2	optional specification of a second set of expression data. See details.
power	soft-thresholding power for network construction.
corFnc	character string giving the correlation function to be used for the adjacency calculation. Recommended choices are "cor" and "bicor", but other functions can be used as well.
corOptions	character string giving further options to be passed to the correlation function

Details

The correlation function will be called with arguments datExpr, datExpr2 plus any extra arguments given in corOptions. If datExpr2 is NULL, the standard correlation functions will calculate the corelation of columns in datExpr.

Value

Adjacency matrix of dimensions n*n, where n is the number of genes in datExpr.

Author(s)

Steve Horvath and Peter Langfelder

References

Bin Zhang and Steve Horvath (2005) "A General Framework for Weighted Gene Co-Expression Network Analysis", Statistical Applications in Genetics and Molecular Biology: Vol. 4: No. 1, Article 17

See Also

adjacency

WGCNA documentation built on Sept. 18, 2024, 5:08 p.m.