OlinkAnalyze (version 4.4.0)

olink_normalization_product_format: Formatting the output of olink_normalization_product for seamless use with downstream analysis functions.

Description

Replaces the NPX values of the non-reference project by the Median Centered or QS Normalized NPX, according to the Bridging Recommendation. Edits the BridgingRecommendation column to indicate whether an assay is NotBridgeable, NotOverlapping, MedianCentering, or QuantileSmoothing bridged. Replaces OlinkID by the concatenation of the Explore HT and Explore 3072 OlinkIDs to record the OlinkIDs from both projects for bridgeable assays. Assays that are NotBridgeable or NotOverlapping retain their original non-reference OlinkIDs and NPX values. Replaces SampleID with the concatenation of SampleID and Project to make unique sample IDs for downstream analysis. Removes internal and external controls. Removes MedianCenteredNPX, QSNormalizedNPX, OlinkID_E3072 columns.

Usage

olink_normalization_product_format(
  df_norm,
  df1,
  df1_project_nr,
  df2,
  df2_project_nr,
  prod_uniq,
  lst_check
)

Value

A "tibble" of Olink data in long format containing both input datasets with the bridged NPX quantifications, with the above modifications.

Arguments

df_norm

A "tibble" of Olink data in long format resulting from the olink_normalization_product function.

df1

First dataset to be used for normalization, pre-normalization. Must match df1 used in olink_normalization product bridging.

df1_project_nr

Project name of first dataset. Must match name used in olink_normalization product bridging.

df2

Second dataset to be used for normalization, pre-normalization. Must match df2 used in olink_normalization product bridging.

df2_project_nr

Project name of second dataset. Must match name used in olink_normalization product bridging.

prod_uniq

Name of products (not_ref, ref)

lst_check

= lst_check

Author

Danai G. Topouza Klev Diamanti

Examples

# \donttest{
# bridge samples
bridge_samples <- intersect(
  x = unique(OlinkAnalyze:::data_ht_small$SampleID),
  y = unique(OlinkAnalyze:::data_3k_small$SampleID)
) |>
  (\(x) x[!grepl("CONTROL", x)])()

# run olink_normalization
df_norm <- olink_normalization(
  df1 = OlinkAnalyze:::data_ht_small,
  df2 = OlinkAnalyze:::data_3k_small,
  overlapping_samples_df1 = bridge_samples,
  df1_project_nr = "Explore HT",
  df2_project_nr = "Explore 3072",
  reference_project = "Explore HT"
)

# generate lst_check
lst_check_3k_ht <- OlinkAnalyze:::olink_norm_input_check(
 df1 = OlinkAnalyze:::data_ht_small,
 df2 = OlinkAnalyze:::data_3k_small,
 overlapping_samples_df1 = bridge_samples,
 overlapping_samples_df2 = NULL,
 df1_project_nr = "Explore HT",
 df2_project_nr = "Explore 3072",
 reference_project = "Explore HT",
 reference_medians = NULL
 )

# format output
OlinkAnalyze:::olink_normalization_product_format(
  df_norm = df_norm,
  df1 = OlinkAnalyze:::data_ht_small,
  df2 = OlinkAnalyze:::data_3k_small,
  df1_project_nr = "Explore HT",
  df2_project_nr = "Explore 3072",
  lst_check = lst_check_3k_ht,
  prod_uniq = c("3k", "HT")
)
# }