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 " |
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 |
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")