WGCNA (version 1.25-1)

scaleFreeFitIndex: Calculation of fitting statistics for evaluating scale free topology fit.

Description

The function scaleFreeFitIndex calculates several indices (fitting statistics) for evaluating scale free topology fit. The input is a vector (of connectivities) k. Next k is discretized into nBreaks number of equal-width bins. Let's denote the resulting vector dk. The relative frequency for each bin is denoted p.dk.

Usage

scaleFreeFitIndex(k, nBreaks = 10, removeFirst = FALSE)

Arguments

k

numeric vector whose components contain non-negative values

nBreaks

positive integer. This determines the number of equal width bins.

removeFirst

logical. If TRUE then the first bin will be removed.

Value

• Data frame with columns
• Rsquared.SFT
  the model fitting index (R.squared) from the following model lm(log.p.dk ~ log.dk)
• slope.SFT
  the slope estimate from model lm(log(p(k))~log(k))
• truncatedExponentialAdjRsquared
  the adjusted R.squared measure from the truncated exponential model given by lm2 = lm(log.p.dk ~ log.dk + dk).