Read and Process SomaLogic adat file
read_somalogic.RdThis 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.
Value
A named list with the following elements:
- data
A matrix of RFU values for experimental samples, with `SampleId` as row names and `SeqId` (from columns containing "seq") as column names.
- samples
A `tibble` containing metadata for experimental samples, with `sample_id` (renamed from `SampleId`) as the first column.
- features
A `tibble` containing feature-level metadata (e.g., protein details), 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` as column names.
- control_metadata
A `tibble` containing metadata for control samples (specifically "Calibrator" samples), with `sample_id` as the first column.
Details
The function performs several validation steps and data transformations:
It first checks if the provided `filepath` points to an `.adat` file.
It uses `SomaDataIO::read_adat()` to import the raw data and `SomaDataIO::is.soma_adat()` to verify its integrity as a SomaLogic object.
It confirms the presence of the crucial `SampleId` column.
Data is separated into experimental "Sample" and "Calibrator" control groups based on the `SampleType` column.
For both sample and control data, RFU values corresponding to "seq" columns are extracted and reshaped into wide matrices with `SampleId` as row names.
Feature metadata is extracted from `attr(df, "Col.Meta")`, and a new `feature_id` column is created (prefixed with "seq." and hyphens replaced by periods).
Sample and control metadata are extracted from `attr(df, "row_meta")`, converted to `tibble`s, renamed, and `sample_id` is relocated to the front. Explicit `tibble::as_tibble()` and `tibble::remove_rownames()` are used to handle potential `SomaDataIO` object intricacies.
Examples
if (FALSE) { # \dontrun{
filepath <- system.file("extdata", "example_data10.adat", package = "SomaDataIO")
somalogic_data <- read_somalogic(filepath)
} # }