This function performs a PCA analysis on the input data and combines it with the sample metadata to perform an ANOVA test to identify significant differences between the groups.

Usage

MetaAnalysis(
  InputData,
  SettingsFile_Sample,
  Scaling = TRUE,
  Percentage = 0.1,
  StatCutoff = 0.05,
  SaveAs_Table = "csv",
  SaveAs_Plot = "svg",
  PrintPlot = TRUE,
  FolderPath = NULL
)

Arguments

InputData: DF with unique sample identifiers as row names and metabolite numerical values in columns with metabolite identifiers as column names. Use NA for metabolites that were not detected. includes experimental design and outlier column.
SettingsFile_Sample: Optional: DF which contains information about the samples, which will be combined with your input data based on the unique sample identifiers used as rownames. Column "Conditions" with information about the sample conditions (e.g. "N" and "T" or "Normal" and "Tumor"), can be used for feature filtering and colour coding in the PCA. Column "AnalyticalReplicate" including numerical values, defines technical repetitions of measurements, which will be summarised. Column "BiologicalReplicates" including numerical values. Please use the following names: "Conditions", "Biological_Replicates", "Analytical_Replicates".Default = NULL
Scaling: Optional: TRUE or FALSE for whether a data scaling is used Default = TRUE
Percentage: Optional: Percentage of top and bottom features to be displayed in the results. Default = 0.1
StatCutoff: Optional: Cutoff for the adjusted p-value of the ANOVA test. Default = 0.05
SaveAs_Table: Optional: File types for the analysis results are: "csv", "xlsx", "txt". Default = "csv"
SaveAs_Plot: Optional: Select the file type of output plots. Options are svg, png, pdf. Default = svg
PrintPlot: Optional: TRUE or FALSE, if TRUE Volcano plot is saved as an overview of the results. Default = TRUE
FolderPath: Optional: Path to the folder the results should be saved at. default: NULL

Value

List of DFs: prcomp results, loadings, Top-Bottom features, annova results, results summary

Examples

Tissue_Norm <- MetaProViz::ToyData("Tissue_Norm")
Res <- MetaProViz::MetaAnalysis(InputData=Tissue_Norm[,-c(1:13)],
                                SettingsFile_Sample= Tissue_Norm[,c(2,4:5,12:13)])
#> The column names of the 'SettingsFile_Sample' contain special character that where removed.