Package index • damR

Data import

ReadFile(): Read and process input data file

QC

QCData(): Run QC on input data

PCA

GetPCA(): Compute PCA and variance explained
PlotPCA(): Plot PCA

Extraction method filtering

FilterExtraction(): Select the best extraction method for each metabolite

Blank filtering

FilterBlanks(): Blank filter data by batch
GetBlankDropTable(): Identify data that falls under the provided threshold by batch across batches
dropBlankFiltered(): Drop data that fails to meet the blank fold change threshold as found by GetBlankDropTable()

Missingness

RemoveMissing(): Remove missing data
IdentifyMissing(): Get metabolites where proportion present is less than a set threshold
PlotMissingness(): Plot missingness heatmap
impute.QRILC(): QRILC imputation

Modelling

DiffMetabolites(): Get differential metabolites with log fold-changes and adjusted pvalues based on input comparison groups

Helpers

MakeTheContrasts(): Produce contrasts from comparisons
FitTheData(): Fit model with limma across all. DiffMetabolites() should be preferred to using this function directly.
pAdjustData(): Multiple testing correction within contrasts. DiffMetabolites() should be preferred to using this function directly.

Plotting

VolcanoData(): Produce volcano plot data for a single contrast
PlotVolcano(): Plot volcano for a single contrast
PlotAllVolcanoes(): Plot volcanoes for all input contrasts