createSampleSubmission: Create a SomaLogic Sample Submission Form
In graumannlab/readat: Functionality to Read and Manipulate SomaLogic ADAT files

Description Usage Arguments Value See Also Examples

View source: R/read-sample-submision-input-files.R

Creates a data table of contents for a SomaLogic sample submission form.

createSampleSubmission(
  slides,
  controls,
  comments,
  samples,
  sampleMatrix = c("EDTA-Plasma", "Sodium Citrate Plasma", "Serum"),
  siteId = "WCQ",
  studyName = "",
  studyId = "",
  runName = "Set A"
)

`slides`	A data frame of slide data, as imported by `readSlides`.
`controls`	A data frame of control data, as imported by `readControls`.
`comments`	A data frame of comment data, as imported by `readComments`.
`samples`	A data frame of sample data, as imported by `readSamples`.
`sampleMatrix`	A string giving the type of samples (plamsa or serum).
`siteId`	A string giving the SomaLogic ID of your site or institution.
`studyName`	A string giving your institution's name for the study.
`studyId`	A string giving the SomaLogic ID of the study
`runName`	A string naming the plate.

A data table with the 96 rows (one plate worth, with each row representing a sample). It contains the following columns:

SampleNumber: One to ninety six.
SlideId: From slides.csv.
Subarray: Position in slide, from 1 to 8.
PlatePosition: Position in plate, from A1 to H12
PercentDilution: Always 40.
BarCode: From controls.csv.
SampleNotes: From controls.csv.
AssayNotes: From controls.csv.
SampleId: From samples.csv.
SampleMatrix: sampleMatrix for samples; blank for controls.
SiteId: siteId for samples; blank for controls.
StudyName: studyName for samples; blank for controls.
TimePoint: Currently blank.
SampleGroup: Currently blank.
SampleDescription: Currently blank.
StudyId: studyId for samples; blank for controls.
RunName: runName for samples; blank for controls.

writeSampleSubmissionForm for a more complete usage example.

# Import the input files
withr::with_dir(
    system.file("extdata", package = "readat"),
    {
        slides <- readSlides()
        controls <- readControls()
        comments <- readComments()
        samples <- readSamples()
    }
)

# Create the sample submission form and write to Excel spreadsheet
submission <- createSampleSubmission(
    slides, controls, comments, samples,
    studyName = "Taheri01", studyId = "WCQ-16-002"
)
str(submission)