single_mod_enrichplot {DDPNA}R Documentation

single_mod_enrichplot

Description

FCS enrichment analysis of a sets of proteins in one module.

Usage

single_mod_enrichplot(module, Mod_Nam, classifiedID,
                      coln = "new.ID", datainf = NULL,
                      plot = TRUE, filename = NULL, ...)

Arguments

module

module information which is getted in Module_inf function.

Mod_Nam

the module name which module will be calculate.

classifiedID

a sets of protein IDs which is ordered by change value/ p value and so on.

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.

plot

a logical value indicating whether draw enrichment variation trend plot.

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.

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")
m5enrich <- single_mod_enrichplot(Module, 5, up, coln="ori.ID")


[Package DDPNA version 0.3.1 Index]