FCSenrichplot | R Documentation |
plot of FCS enrichment analysis
FCSenrichplot(FCSenrich, count = 1, p = 0.05, filter = "p", plot = TRUE, filename = NULL,filetype = "pdf", ...)
FCSenrich |
FCS enrichment information which is getted in |
count |
a numeric value. Module will choosed when countnumber is larger than count value . |
p |
a numeric value. Module will choosed when any Fisher's extract test p value is less than count value . |
filter |
filter methods.
This must be (an abbreviation of) one of the strings " |
plot |
a logical value indicating whether draw enrichment variation trend plot. |
filename |
the filename of plot. The default value is |
filetype |
the file type of plot. the type should be one of "eps", "ps", "tex" (pictex), "pdf", "jpeg", "tiff", "png", "bmp", "svg" or "wmf" (windows only). |
... |
Other arguments. |
Kefu Liu
data(imputedData) data(net) data <- imputedData logD <- data$log2_value rownames(logD) <- data$inf$ori.ID group <- gsub("[0-9]+","", colnames(logD)) Module <- Module_inf(net, data$inf) pos<-which(Module$moduleNum %in% c(11:13)) up <- changedID(logD[pos,], group, vs.set2 = "ad",vs.set1 = "ctl", rank = "foldchange",anova = FALSE, Padj = "none",cutoff = 1, datatype = "log2",fctype = "up") FCSenrich <- Module_Enrich(Module[pos,], up, coln="ori.ID") FCSenrich <- FCSenrichplot(FCSenrich)
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