readAdat: Read a SomaLogic data file
In graumannlab/readat: Functionality to Read and Manipulate SomaLogic ADAT files

Description Usage Arguments Value Author(s) Examples

Reads a SomaLogic ADAT data file.

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

`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.

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.

Richard Cotton

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

# For compatibility with rest of Bioconductor you may want an ExpressionSet
as.ExpressionSet(wideSomaData)