R/ClearScatterplot.R
ClearScatterplot_MAE.Rd
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
)
A MultiAssayExperiment object containing the assay data.
The name of the assay to use for plotting.
The name of the column containing expression values.
The name of the column containing the negative log p-values.
Threshold for high log2 fold change values.
Threshold for low log2 fold change values.
Threshold for -log10 p-value.
An object of class ClearScatterplot.
# Assuming 'mae' is a MultiAssayExperiment object with appropriate assays
scatterplotObject <- ClearScatterplot_MAE(mae, "assayName")
#> Error in eval(expr, envir, enclos): object 'mae' not found