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Filter Assay Based on Limit of Detection (LOD)

lod_filter.Rd

Filters the assay data of a SummarizedExperiment by comparing intensities against a specific Limit of Detection (LOD). The LOD values can be sourced either from a metadata column (rowData) or a specific reference sample (e.g., a Buffer column in the assay).

Usage

lod_filter(se, lod_col = "Buffer")

# S4 method for class 'SummarizedExperiment'
lod_filter(se, lod_col = "Buffer")

Arguments

se

A SummarizedExperiment object.

lod_col

A character string indicating where to find the LOD values. The function first searches rowData(se), then searches the column names of the assay (e.g., a specific buffer sample). Defaults to "Buffer".

Value

A SummarizedExperiment object where values below the defined LOD are replaced with NA.

Functions

  • lod_filter(SummarizedExperiment): Method for SummarizedExperiment objects