modpcomp: modpcomp

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

Description

extract module pca component

Usage

modpcomp(data, colors, nPC = 2,
         plot = FALSE, filename = NULL, group = NULL)

Arguments

data	protein quantification data. column is sample. row is protein ID.
colors	protein and module information. which is calculated in WGCNA package.
nPC	how many PCA component will saved.
plot	a logical value indicating whether draw PCA plot. This function is based on https://github.com/vqv/ggbiplot which had to be copied to DHMDA because Bioconductor does not support remote dependencies from GitHub.
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.
group	sample group information.

Author(s)

Kefu Liu

Examples

rm(list = ls())
library(DDPNA)
data(net)
data(imputedData)
data <- imputedData
logD <- data$log2_value
rownames(logD) <- data$inf$ori.ID
Module_PCA <- modpcomp(logD, net$colors)

# if plot PCA and plot module 6 PCA
group <- gsub("[0-9]+", "", colnames(logD))
pos <- which(net$colors == 6)
Module_PCA <- modpcomp(logD[pos,], net$colors[pos], plot = TRUE, group = group)

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