diffAnaVolcanoplot {DAPAR} | R Documentation |
Plots a volcanoplot after the differential analysis.
Typically, the log of Fold Change is represented on the X-axis and the
log10 of the p-value is drawn on the Y-axis. When the threshold_pVal
and the threshold_logFC
are set, two lines are drawn respectively on
the y-axis and the X-axis to visually distinguish between differential and
non differential data.
diffAnaVolcanoplot(logFC = NULL, pVal = NULL, threshold_pVal = 1e-60, threshold_logFC = 0, conditions = NULL, colors = NULL)
logFC |
A vector of the log(fold change) values of the differential analysis. |
pVal |
A vector of the p-value values returned by the differential analysis. |
threshold_pVal |
A floating number which represents the p-value that separates differential and non-differential data. |
threshold_logFC |
A floating number which represents the log of the Fold Change that separates differential and non-differential data. |
conditions |
A list of the names of condition 1 and 2 used for the differential analysis. |
colors |
xxx |
A volcanoplot
Florence Combes, Samuel Wieczorek
require(DAPARdata) data(Exp1_R25_pept) obj <- Exp1_R25_pept[1:1000] keepThat <- mvFilterGetIndices(obj, 'wholeMatrix', ncol(obj)) obj <- mvFilterFromIndices(obj, keepThat) qData <- Biobase::exprs(obj) sTab <- Biobase::pData(obj) limma <- limmaCompleteTest(qData,sTab) diffAnaVolcanoplot(limma$logFC[,1], limma$P_Value[,1])