SoftThresholdScaleGraph {DDPNA}

SoftThresholdScaleGraph

Description

pick soft thresholding powers for WGCNA analysis and plot

Usage

SoftThresholdScaleGraph(data,
                        xlab = "Soft Threshold (power)",
                        ylab = "Scale Free Topology Model Fit, signed R^2",
                        main = "Scale independence",
                        filename = NULL,...)

Arguments

data

protein quantification data. row is sample. column is protein ID.

xlab

x axis label

ylab

y axis label

main

plot title

filename

the filename of plot. The default value is NULL which means no file saving. The plot will be saved to "plot" folder and saved in pdf format.

...

Other arguments in function pickSoftThreshold in WGCNA package.

Details

pick soft thresholding powers for WGCNA analysis and plot. The function is also can replaced by "pickSoftThreshold" function in WGCNA package.

Value

A list with the following components:

powerEstimate

the lowest power fit for scale free topology.

fitIndices

a data frame containing the fit indices for scale free topology.

Author(s)

Kefu Liu

See Also

pickSoftThreshold in WGCNA package.

Examples

#it will take some times
data(imputedData)
data <- imputedData
logD <- data$log2_value
rownames(logD) <- data$inf$ori.ID
if (requireNamespace("WGCNA", quietly = TRUE))
  sft <- SoftThresholdScaleGraph(t(logD))