Module_Enrich: Module_Enrich

In DDPNA: Disease-Drived Differential Proteins Co-Expression Network Analysis

Module_Enrich

Description

Enrichment analysis of a sets of proteins in all modules. The function offered two enrichment methods:ORA and FCS.

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.

Value

a list contains classifiedID enrichment information.

Counts	the counts of classifiedID in module.
module.size	the number of module ID
module.name	module name
precent	counts divided module.size
p	enrichment p value in each module
p.adj	enrichment p.adj value in each module
Z.score	Z score is -log2 P value.

Author(s)

Kefu Liu

Examples

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")

DDPNA documentation built on May 17, 2022, 5:05 p.m.