This script allows you to perform metabolite clustering analysis and computes clusters of metabolites based on regulatory rules between two conditions (e.g. KO versus WT in Hypoxia = Cond1 and KO versus WT in Normoxia = Cond2).
Usage
MCA_2Cond(
InputData_C1,
InputData_C2,
SettingsInfo_C1 = c(ValueCol = "Log2FC", StatCol = "p.adj", StatCutoff = 0.05,
ValueCutoff = 1),
SettingsInfo_C2 = c(ValueCol = "Log2FC", StatCol = "p.adj", StatCutoff = 0.05,
ValueCutoff = 1),
FeatureID = "Metabolite",
SaveAs_Table = "csv",
BackgroundMethod = "C1&C2",
FolderPath = NULL
)Arguments
- InputData_C1
DF for your data (results from e.g. DMA) containing metabolites in rows with corresponding Log2FC and stat (p-value, p.adjusted) value columns.
- InputData_C2
DF for your data (results from e.g. DMA) containing metabolites in rows with corresponding Log2FC and stat (p-value, p.adjusted) value columns.
- SettingsInfo_C1
Optional: Pass ColumnNames and Cutoffs for condition 1 including the value column (e.g. Log2FC, Log2Diff, t.val, etc) and the stats column (e.g. p.adj, p.val). This must include: c(ValueCol=ColumnName_InputData_C1,StatCol=ColumnName_InputData_C1, StatCutoff= NumericValue, ValueCutoff=NumericValue) Default=c(ValueCol="Log2FC",StatCol="p.adj", StatCutoff= 0.05, ValueCutoff=1)
- SettingsInfo_C2
Optional: Pass ColumnNames and Cutoffs for condition 2 includingthe value column (e.g. Log2FC, Log2Diff, t.val, etc) and the stats column (e.g. p.adj, p.val). This must include: c(ValueCol=ColumnName_InputData_C2,StatCol=ColumnName_InputData_C2, StatCutoff= NumericValue, ValueCutoff=NumericValue)Default=c(ValueCol="Log2FC",StatCol="p.adj", StatCutoff= 0.05, ValueCutoff=1)
- FeatureID
Optional: Column name of Column including the Metabolite identifiers. This MUST BE THE SAME in each of your Input files. Default="Metabolite"
- SaveAs_Table
Optional: File types for the analysis results are: "csv", "xlsx", "txt" default: "csv"
- BackgroundMethod
Optional: Background method C1|C2, C1&C2, C2, C1 or * Default="C1&C2"
- FolderPath
Optional: Path to the folder the results should be saved at. default: NULL