R: Comparing two biological conditions in a metabolomics data...
TwoGroup
R Documentation
Comparing two biological conditions in a metabolomics data matrix
Description
This function computes fold changes, t statistics, p-values, and
adjusted p-values for each metabolite given a series of replicates and two biological conditions.
A log transformed data frame in the input data format. See metabolomics for details.
alternative
A character string specifying the alternative hypothesis for the t tests. This should be one of "two.sided", "greater" or "less". The default is set to "two.sided".
paired
A logical indicating whether the t-test should be paired
or not. The default is set to "FALSE".
padjmethod
A character string specifying p-value adjustment method for multiple comparisons. Must be one of "bonferroni", "holm" (Holm 1979), "hochberg" (Hochberg 1988), "hommel" (Hommel 1988), "BH" (Benjamini and Hochberg 1995), "BY" (Benjamini and Yekutieli 2001), or "none". The default method is set to "BH".
saveoutput
A logical indicating whether the output should be saved.
If TRUE the output will be saved as a .csv file.
outputname
The name of the output file if the output has to be
saved.
...
Further arguments to be passed to or from methods.
Value
The result is an object of class "results".
output
A matrix with t statistics, p-values, adjusted p-values, fold changes, and standard errors.
Author(s)
Alysha M De Livera, Jairus B Bowne
References
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.