unsignedAdjacency: 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'")

Value

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

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

Author

Steve Horvath and Peter Langfelder

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.

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