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Apply Limit of Detection Threshold

apply_min_intenisty.Rd

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.

Functions

  • apply_min_intenisty(SummarizedExperiment): Method for SummarizedExperiment objects

Examples

# Create a mock SummarizedExperiment
counts <- matrix(c(10, 5, 2, 8, 1, 15), nrow = 3, ncol = 2)
se <- SummarizedExperiment(assays = list(counts = counts))
#> Error in SummarizedExperiment(assays = list(counts = counts)): could not find function "SummarizedExperiment"

# Apply LOD of 6
se_filtered <- applyLOD(se, lod = 6)
#> Error in applyLOD(se, lod = 6): could not find function "applyLOD"
assay(se_filtered)
#> Error in assay(se_filtered): could not find function "assay"