Apply Limit of Detection Threshold

Filters assay data by converting values below a specified Limit of Detection (LOD) to NA.

Usage

apply_min_intenisty(object, lod)

# S4 method for class 'SummarizedExperiment'
apply_min_intenisty(object, lod)

Arguments

object

A SummarizedExperiment object containing a single proteomics assay.

lod

A single numeric value representing the Limit of Detection. Intensities below this value will be replaced with NA.

Value

The original object with the assay matrix updated to contain NA values where intensities were below the lod.

Examples

# Create a mock SummarizedExperiment
counts <- matrix(c(10, 5, 2, 8, 1, 15), nrow = 3, ncol = 2)
se <- SummarizedExperiment::SummarizedExperiment(assays = list(counts = counts))

# Apply LOD of 6
se_filtered <- apply_min_intenisty(se, lod = 6)
SummarizedExperiment::assay(se_filtered)
#>      [,1] [,2]
#> [1,]   10    8
#> [2,]   NA   NA
#> [3,]   NA   15