readAdat {readat} | R Documentation

## Read a SomaLogic data file

### Description

Reads a SomaLogic ADAT data file.

### Usage

    readAdat(file, keepOnlyPasses = TRUE, keepOnlySamples = TRUE,
      dateFormat = "%Y-%m-%d", verbose = getOption("verbose"))

### Arguments

`file` | A string containing the path to the file to be read.
`keepOnlyPasses` | A logical value indicating whether or not to keep only the rows and columns where the data quality was considered to be passable.
`keepOnlySamples` | A logical value indicating whether or not to keep only the rows containing actual samples (as opposed to QC, buffer, and calibrator samples).
`dateFormat` | A string describing the format of the dates contained in the file's metadata. See `strptime` for how to specify these.
`verbose` | Logical value indicating whether (lots of) diagnostic messages should be shown.

### Value

An object of class `WideSomaLogicData`, which inherits from `data.table`. The return value consists of a data frame where each row represents a sample. Initial columns contain sample metadata and later columns contain intensities of proteins. The specific metadata columns are not fixed, but the most useful ones described below should always be present.

SampleUniqueID

  A unique identifier for the sample.

Subject_ID

  A unique identifier for the person being sampled.

RowCheck

  This should have the value "PASS" if the data quality is acceptable.

Columns of proteins intensities have a name beginning `SeqId.`. Return value also has three attributes.

SequenceData

  A data frame.

Metadata

  A list of experimental metadata values.

Checksum

  A SHA1 checksum to ensure file integrity.

### Author(s)

Richard Cotton

### Examples

    somaFile <- extractSampleData()
    wideSomaData <- readAdat(somaFile)
    str(wideSomaData, list.len = 35)
    unlink(somaFile)

[Package readat version 1.8.0 Index]