Module_Enrich: Module_Enrich

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

Description

Enrichment analysis of a sets of proteins in all modules.

Usage

Module_Enrich(module, classifiedID, enrichtype = "FCS",
              coln = "new.ID", datainf = NULL, p.adj.method = "BH")

Arguments

module	module information which is getted in Module_inf function.
classifiedID	a sets of protein IDs which is ordered by change value/ p value and so on.
enrichtype	enrichment method. This must be (an abbreviation of) one of the strings "FCS","ORA". "FCS" means analyzes step-by-step a proteins list which is ordered by change ratio/ p value and so on. "ORA" means analyzes a proteins list by Fisher's extract test.
coln	column name of module contains protein IDs. it could be matched with "classifiedID"
datainf	proteomic data protein ID information. The default value is "NULL". which is means that the "classifiedID" come from proteomic information is the same as the module construction proteomic information. If they are different, proteomic data information should be given.
p.adj.method	p adjust methods of multiple comparisons. it can seen in p.adjust.methods.

Author(s)

Kefu Liu

Examples

rm(list = ls())
library(DDPNA)
data(net)
data(imputedData)
data <- imputedData
logD <- data$log2_value
rownames(logD) <- data$inf$ori.ID
group <- gsub("[0-9]+","", colnames(logD))
Module <- Module_inf(net, data$inf)
up <- changedID(logD, group, vs.set2 = "ad",vs.set1 = "ctl",
              rank = "foldchange",anova = FALSE, Padj = "none",cutoff = 1,
              datatype = "log2",fctype = "up")
FCSenrich <- Module_Enrich(Module, up, coln="ori.ID")

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