Find metabolites with high variability across total pool samples

Usage

PoolEstimation(
  InputData,
  SettingsFile_Sample = NULL,
  SettingsInfo = NULL,
  CutoffCV = 30,
  SaveAs_Plot = "svg",
  SaveAs_Table = "csv",
  PrintPlot = TRUE,
  FolderPath = NULL
)

Arguments

InputData: DF which contains 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. Can be either a full dataset or a dataset with only the pool samples.
SettingsFile_Sample: Optional: DF which contains information about the samples when a full dataset is inserted as Input_data. Column "Conditions" with information about the sample conditions (e.g. "N" and "T" or "Normal" and "Tumor"), has to exist.Default = NULL
SettingsInfo: Optional: NULL or Named vector including the Conditions and PoolSample information (Name of the Conditions column and Name of the pooled samples in the Conditions in the Input_SettingsFile) : c(Conditions="ColumnNameConditions, PoolSamples=NamePoolCondition. If no Conditions is added in the Input_SettingsInfo, it is assumed that the conditions column is named 'Conditions' in the Input_SettingsFile. ). Default = NULL
CutoffCV: Optional: Filtering cutoff for high variance metabolites using the Coefficient of Variation. Default = 30
SaveAs_Plot: Optional: Select the file type of output plots. Options are svg, png, pdf or NULL. Default = svg
SaveAs_Table: Optional: File types for the analysis results are: "csv", "xlsx", "txt", ot NULL default: "csv"
PrintPlot: Optional: If TRUE prints an overview of resulting plots. Default = TRUE
FolderPath: Optional: Path to the folder the results should be saved at. default: NULL

Value

List with two elements: DF (including input and output table) and Plot (including all plots generated)

Examples

Intra <- ToyData("IntraCells_Raw")
Res <- PoolEstimation(InputData=Intra[ ,-c(1:3)],
                                SettingsFile_Sample=Intra[ , c(1:3)],
                                SettingsInfo = c(PoolSamples = "Pool", Conditions="Conditions"))
#> Error in ggplot2::autoplot(stats::prcomp(as.matrix(InputData), scale. = as.logical(Scaling)),     data = InputPCA, colour = Param_Col, fill = Param_Col, shape = Param_Sha,     size = 3, alpha = 0.8, label = T, label.size = 2.5, label.repel = TRUE,     loadings = as.logical(ShowLoadings), loadings.label = as.logical(ShowLoadings),     loadings.label.vjust = 1.2, loadings.label.size = 2.5, loadings.colour = "grey10",     loadings.label.colour = "grey10"): Objects of class <prcomp> are not supported by autoplot.
#> ℹ Have you loaded the required package?