Tests: Standard tests

In AlzbetaG/Metabol: The statistical analysis of metabolomic data

Description

Makes Shapiro-Wilk test, ANOVA, Kruskal-Wallis test, t-test for every variable and Wilcoxon test for every variable.

Usage

Tests(data, name, groupnames, tsf = "clr", pair = FALSE, QCs = FALSE)

Arguments

data	Data table with variables (metabolites) in columns. Samples in rows are sorted according to specific groups.
name	A character string or expression indicating a name of data set. It occurs in names of every output.
groupnames	A character vector defining specific groups in data. Every string must be specific for each group and they must not overlap.
tsf	Data transformation must be defined by "clr" (default), "log", "log10", "PQN", "lnPQN", "pareto" or "none". See Details.
pair	logical. If TRUE then the paired tests are done. Default is FALSE.
QCs	logical. If FALSE (default) quality control samples (QCs) are automatically distinguished and skipped.

Details

Data transformation: with "clr" clr trasformation is used (see References), with "log" natural logarithm is used, with "log10" decadic logarithm is used, with "pareto" data are only scaled by Pareto scaling, with "PQN" probabilistic quotient normalization is done, with "lnPQN" natural logarithm of PQN transformed data is done, with "none" no tranformation is done.

Value

Excel file with p-values from Shapiro-Wilk test, ANOVA, Kruskal-Wallis test, t-test for every variable and Wilcoxon test for every variable and their summary.

References

Aitchison, J. (1986) The Statistical Analysis of Compositional Data Monographs on Statistics and Applied Probability. Chapman & Hall Ltd., London (UK). p. 416.

Examples

data=metabol
name="Metabolomics"    #name of the project
groupnames=c("Con","Pat","QC")
Tests(data,name,groupnames)

AlzbetaG/Metabol documentation built on May 31, 2019, 12:39 a.m.