Preparation of a proteomics analysis data set

Usage

prepare_proteomics_analysis_dataset(
  participant_data,
  protein_data,
  protein_meta_data,
  plate_correction = c("none", "median-subcohort", "mean-subcohort"),
  scaling = c("none", "center-subcohort", "scale-subcohort", "center", "scale", "rint"),
  id = "csid"
)

Arguments

participant_data

A data frame of participant data

protein_data

Protein data produced by prepare_olink_data() or prepare_somascan_data().

protein_meta_data

Corresponding protein meta data produed by prepare_olink_meta_data() or prepare_somascan_meta_data().

plate_correction

Type of plate correction to apply:

"none" (default)
"median-subcohort": For each protein, subtract the plate median (of subcohort values) and add the overall median (of subcohort values).
"mean-subcohort": For each protein, subtract the plate mean (of subcohort values) and add the overall mean (of subcohort values).

scaling

Scaling to apply to values for each protein:

"none" (default)
"center-subcohort": Subtract the overall mean of subcohort values.
"scale-subcohort": Subtract the overall mean and divide by the sample standard deviation of subcohort values.
"center": Subtract the overall mean.
"scale": Subtract the overall mean and divide by the sample standard deviation.
"rint": Rank inverse normal transformation.

id

Name of column used to join participant_data and protein_data. (Default: "csid")