Description Usage Arguments Value Author(s) References Examples
View source: R/TwoGroupPlots.r
Produces plots for visualising differential metabolites.
1 2 | TwoGroupPlots(datamat, tstats, foldchanges, pvalues,
padjmethod = "BH", fcutoff = log(2), pcutoff = 0.05, cexval = 0.7)
|
datamat |
A numerical data matrix with samples in rows and metabolites in columns |
tstats |
A vector of t statistics. |
foldchanges |
A vector of fold changes. |
pvalues |
A vector of corresponding p-values. |
padjmethod |
A character string specifying p-value adjustment method for multiple comparisons. Must be one of " |
fcutoff |
A numeric indicating the fold change cut off. The default is set to 2. |
pcutoff |
A numeric indicating the adjusted p-value cut off. The default is set to 0.05. |
cexval |
The font size of the text labels. |
A list containing:
IncreasedMets |
Names of increased metabolites. |
DecreasedMets |
Names of decreased metabolites. |
DifferentialMets |
Names of all differential metabolites. |
Alysha M De Livera, Jairus B Bowne
Benjamini, Y., Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological) 57(1): 289-300.
Benjamini, Y., Yekutieli, D. (2001) The Control of the False Discovery Rate in Multiple Testing under Dependency. The Annals of Statistics 29(4): 1165-1188.
Hochberg, Y. (1988) A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75(4): 800-802.
Holm, S. (1979) A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics 6(2): 65-70.
Hommel, G. (1988) A stagewise rejective multiple test procedure based on a modified Bonferroni test. Biometrika 75(2): 383-386.
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