changedID: changedID

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

Description

extract significant differential protein

Usage

changedID(relative_value, group, vs.set2, vs.set1 = "WT",
          rank = "none", anova = TRUE, anova.cutoff = 0.05,
          T.cutoff = 0.05, Padj = "fdr",
          cutoff = 1.5, datatype = c("none","log2"), fctype = "all",...)

Arguments

relative_value	protein quantification data
group	sample group information
vs.set2	compared group 2 name
vs.set1	compared group 1 name
rank	order by which type. This must be (an abbreviation of) one of the strings "none","foldchange", "anova","t"
anova	a logical value indicating whether do anova analysis.
anova.cutoff	a numberic value indicated that anova test p value upper limit.
T.cutoff	a numberic value indicated that t.test p value upper limit.
Padj	p adjust methods of multiple comparisons. it can seen in p.adjust.methods.
cutoff	a numberic value indicated that foldchange lower limit.
datatype	The quantification data is normal data or log2 data.
fctype	foldchange is ordered by up-regulated or down-regulated or changed
...	Other arguments.

Details

extract significant differential protein ID based on foldchange, t.test p value, anova p value.

Author(s)

Kefu Liu

Examples

rm(list = ls())

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

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