SoftThresholdScaleGraph: SoftThresholdScaleGraph

In liukf10/TEST: Disease-Drived Differential Proteins and Proteome-Wide Co-Expression Network Associated Analysis

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.

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

rm(list = ls())
library(DDPNA)
data(imputedData)
data <- imputedData
logD <- data$log2_value
rownames(logD) <- data$inf$ori.ID
if (requireNamespace("WGCNA", quietly = TRUE))
  sft <- SoftThresholdScaleGraph(t(logD))

liukf10/TEST documentation built on May 20, 2019, 12:59 a.m.