Constructor function for creating an instance of the ClearScatterplot class from a MultiAssayExperiment object. This function performs differential expression analysis using limma.

ClearScatterplot_MAE(
  mae,
  assayName = NULL,
  logFoldChange = "log2fc",
  negativeLogPValue = "negLog10p",
  highLog2fc = 0.585,
  lowLog2fc = -0.585,
  negLog10pValue = 1.301
)

Arguments

mae

A MultiAssayExperiment object containing the assay data.

assayName

The name of the assay to use for plotting.

logFoldChange

The name of the column containing expression values.

negativeLogPValue

The name of the column containing the negative log p-values.

highLog2fc

Threshold for high log2 fold change values.

lowLog2fc

Threshold for low log2 fold change values.

negLog10pValue

Threshold for -log10 p-value.

Value

An object of class ClearScatterplot.

Examples

# Assuming 'mae' is a MultiAssayExperiment object with appropriate assays
scatterplotObject <- ClearScatterplot_MAE(mae, "assayName")
#> Error in eval(expr, envir, enclos): object 'mae' not found