olink_lod: Calculate LOD using Negative Controls or Fixed LOD

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Calculate LOD using Negative Controls or Fixed LOD

Description

Calculate LOD using Negative Controls or Fixed LOD

Usage

olink_lod(data, lod_file_path = NULL, lod_method = "NCLOD")

Arguments

data	npx data file
lod_file_path	location of lod file from Olink. Only needed if lod_method = "FixedLOD" or "Both". Default NULL.
lod_method	method for calculating LOD using either "FixedLOD" or negative controls ("NCLOD"), or both ("Both"). Default NCLOD.

Value

A dataframe with 2 additional columns, LOD and PCNormalizedLOD if lod_method is FixedLOD or NCLOD. When Normalization = "Plate Control", LOD and PCNormalizedLOD are identical.

If lod_method is "Both", 4 additional columns will be added:

• NCLOD - LOD calculated from negative controls and normalized based on normalization column

• NCPCNormalizedLOD - PC Normalized LOD calculated from negative controls

• FixedLOD - LOD calculated from fixed LOD file and normalized based on normalization column

• FixedPCNormalizedLOD - PC Normalized LOD calculated from fixed LOD file

Examples

## Not run: 
   \donttest{
  try({ # This will fail if the files do not exist.

  # Import NPX data
    npx_data <- read_NPX("path/to/npx_file")

  # Estimate LOD from negative controls
    npx_data_lod_NC <- olink_lod(data = npx_data,  lod_method = "NCLOD")

  # Estimate LOD from fixed LOD
  ## Locate the fixed LOD file
    lod_file_path <- "path/to/lod_file"

    npx_data_lod_Fixed <- olink_lod(data = npx_data,
                                    lod_file_path = lod_file_path,
                                    lod_method = "FixedLOD")
     })
  }

## End(Not run)

OlinkAnalyze documentation built on April 4, 2025, 3:26 a.m.