changedID {DDPNA}R Documentation

changedID

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.

Value

a vector of protein ID information.

Author(s)

Kefu Liu

Examples

data(imputedData)
data <- imputedData
logD <- data$log2_value
rownames(logD) <- data$inf$ori.ID
group <- gsub("[0-9]+","", colnames(logD))
up <- changedID(logD[201:260,], group, vs.set2 = "ad", vs.set1 = "ctl",
              rank = "foldchange",anova = FALSE, Padj = "none", cutoff = 1,
              datatype = "log2", fctype = "up")


[Package DDPNA version 0.3.1 Index]