Read and Process SomaLogic adat file

This function reads and processes a commercial SomaLogic `.adat` file. It extracts RFU (Relative Florecent Units) data for samples and controls, along with their respective metadata and feature (protein) metadata. The function returns a structured list suitable for further analysis.

Usage

read_somalogic(filepath, return_Omiprep = FALSE)

Arguments

filepath

A string specifying the path to the SomaLogic `.adat` file.

return_Omiprep

logical, if TRUE (default) return a Omiprep object, if FALSE return a list.

Value

A omiprep object or a named list with the following elements:

data

A matrix of RFU values for experimental samples, with `SampleId` as row names and `SeqId` columns as column names.

samples

A data frame containing metadata for experimental samples, with `sample_id` renamed from `SampleId`.

features

A data frame containing feature-level metadata, including a newly created `feature_id` column derived from `SeqId`.

controls

A matrix of RFU values for control samples, specifically "Calibrator" samples, with `SampleId` as row names and `SeqId` columns as column names. If duplicate control `SampleId` values are present, control `SampleId` is replaced with `paste0(SampleId, "_", SlideId)`.

control_metadata

A data frame containing metadata for control samples, specifically "Calibrator" samples, with `sample_id` renamed from `SampleId`.