changedID | R Documentation |
extract significant differential protein
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",...)
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. |
extract significant differential protein ID based on foldchange, t.test p value, anova p value.
a vector of protein ID information.
Kefu Liu
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")
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