readAdat {readat} | R Documentation |
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 |
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.
A unique identifier for the sample.
A unique identifier for the person being sampled.
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.
A data frame.
A list of experimental metadata values.
A SHA1 checksum to ensure file integrity.
Richard Cotton
somaFile <- extractSampleData() wideSomaData <- readAdat(somaFile) str(wideSomaData, list.len = 35) unlink(somaFile)