olink_normalization_n: Bridge and/or subset normalization of all proteins among...

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Bridge and/or subset normalization of all proteins among multiple NPX projects.

Description

This function normalizes pairs of NPX projects (data frames) using shared samples or subsets of samples.

Usage

olink_normalization_n(norm_schema)

Arguments

norm_schema

A tibble with more than 1 rows and (strictly) the following columns: "order", "name", "data", "samples", "normalization_type", "normalize_to". See "Details" for the structure of the data frame (required)

Details

This function is a wrapper of olink_normalization_bridge and olink_normalization_subset.

The input of this function is a tibble that contains all the necessary information to normalize multiple NPX projects. This tibble is called the normalization schema. The basic idea is that every row of the data frame is a separate project to be normalized. We assume that there is always one baseline project that does not normalize to any other. All other project normalize to one or more projects. The function handles projects that are normalized in a chain, for example:

• 1. project 2 normalizes to project 1, and project 3 normalizes to project 2.

• 2. project 2 normalizes to project 1, and project 3 normalizes to the combined data frame of projects 1 and 2 (that is already normalized).

The function can also handle a mixed schema of bridge and subset normalization.

Specifications of the normalization schema data frame:

• order: should strictly be a numeric or integer array with unique identifiers for each project. It is necessary that this array starts from 1 and that it contains no NAs.

• name: should strictly be a character array with unique identifiers for each project. Each entry should represent the name of the project located in the same row. No NAs are allowed.

• data: a named list of NPX data frames representing the projects to be normalized. Names of the items of the list should be identical to "names". No NAs are allowed.

• samples: a two-level nested named list of sample identifiers from each NPX project from "data". Names of the first level of the nested list should be identical to "names" and to the names of the list from "data". Projects that will be used only as reference should have their corresponding element in the list as NA, while all other projects should contain a named list of 2 arrays containing identifiers of samples to be used for the calculation of adjustment factor. The names of the two arrays should be DF1 and DF2 corresponding to the reference project and the project in the current row, respectively. For bridge normalization arrays should be of equal length and the index of each entry should correspond to the same sample. For subset normalization arrays do not need to be of equal length and the order the samples appear in does not matter. DF1 might contain sample identifiers from more than one project as long as the project in the current row is to be normalized to multiple other projects.

• normalization_type: a character array containing the flags "Bridge" or "Subset". Projects that will be used only as reference should have their corresponding element in the array as NA, while all other projects should contain a flag. For the time being the flag "Median" is not supported.

• normalize_to: a character array pointing to the project this project is to be normalized to. Elements of the array should be exclusively from the "order" column. Elements of the array may be comma-separated if the project is to be normalized to multiple projects.

Value

A "tibble" of NPX data in long format containing normalized NPX values, including adjustment factors and name of project.

Examples

#### Bridge normalization of two projects

# prepare datasets
npx_df1 <- npx_data1 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")
npx_df2 <- npx_data2 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")

# Find overlapping samples, but exclude Olink control
overlap_samples <- dplyr::intersect(unique(npx_df1$SampleID),
                                    unique(npx_df2$SampleID))
overlap_samples_list <- list("DF1" = overlap_samples,
                             "DF2" = overlap_samples)

# create tibble for input
norm_schema_bridge <- dplyr::tibble(
  order              = c(1, 2),
  name               = c("NPX_DF1", "NPX_DF2"),
  data               = list("NPX_DF1" = npx_df1,
                            "NPX_DF2" = npx_df2),
  samples            = list("NPX_DF1" = NA_character_,
                            "NPX_DF2" = overlap_samples_list),
  normalization_type = c(NA_character_, "Bridge"),
  normalize_to       = c(NA_character_, "1")
)

# normalize
olink_normalization_n(norm_schema = norm_schema_bridge)

#### Subset normalization of two projects

# datasets
npx_df1 <- npx_data1 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")
npx_df2 <- npx_data2 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")

# Find a suitable subset of samples from both projects, but exclude Olink
# controls and samples that fail QC.
df1_samples <- npx_df1 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::group_by(SampleID) |>
  dplyr::filter(all(QC_Warning == 'Pass')) |>
  dplyr::pull(SampleID) |>
  unique() |>
  sample(size = 16, replace = FALSE)
df2_samples <- npx_df2 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::group_by(SampleID) |>
  dplyr::filter(all(QC_Warning == 'Pass')) |>
  dplyr::pull(SampleID) |>
  unique() |>
  sample(size = 16, replace = FALSE)

# create named list
subset_samples_list <- list("DF1" = df1_samples,
                            "DF2" = df2_samples)

# create tibble for input
norm_schema_subset <- dplyr::tibble(
  order              = c(1, 2),
  name               = c("NPX_DF1", "NPX_DF2"),
  data               = list("NPX_DF1" = npx_df1,
                            "NPX_DF2" = npx_df2),
  samples            = list("NPX_DF1" = NA_character_,
                            "NPX_DF2" = subset_samples_list),
  normalization_type = c(NA_character_, "Subset"),
  normalize_to       = c(NA_character_, "1")
)

# Normalize
olink_normalization_n(norm_schema = norm_schema_subset)

#### Subset normalization  of two projects using all samples

# datasets
npx_df1 <- npx_data1 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")
npx_df2 <- npx_data2 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")

# Find a suitable subset of samples from both projects, but exclude Olink
# controls and samples that fail QC.
df1_samples_all <- npx_df1 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::group_by(SampleID) |>
  dplyr::filter(all(QC_Warning == 'Pass')) |>
  dplyr::pull(SampleID) |>
  unique()
df2_samples_all <- npx_df2 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::group_by(SampleID) |>
  dplyr::filter(all(QC_Warning == 'Pass')) |>
  dplyr::pull(SampleID) |>
  unique()

# create named list
subset_samples_all_list <- list("DF1" = df1_samples_all,
                                "DF2" = df2_samples_all)

# create tibble for input
norm_schema_subset_all <- dplyr::tibble(
  order              = c(1, 2),
  name               = c("NPX_DF1", "NPX_DF2"),
  data               = list("NPX_DF1" = npx_df1,
                            "NPX_DF2" = npx_df2),
  samples            = list("NPX_DF1" = NA_character_,
                            "NPX_DF2" = subset_samples_all_list),
 normalization_type = c(NA_character_, "Subset"),
 normalize_to       = c(NA_character_, "1")
)

# Normalize
olink_normalization_n(norm_schema = norm_schema_subset_all)

#### Multi-project normalization using bridge and subset samples

## NPX data frames to bridge
npx_df1 <- npx_data1 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")

npx_df2 <- npx_data2 |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")

# manipulating the sample NPX datasets to create another two random ones
npx_df3 <- npx_data2 |>
  dplyr::mutate(SampleID = paste(SampleID, "_mod", sep = ""),
                PlateID = paste(PlateID, "_mod", sep = ""),
                NPX = sample(x = NPX, size = dplyr::n(), replace = FALSE)) |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")

npx_df4 <- npx_data1 |>
  dplyr::mutate(SampleID = paste(SampleID, "_mod2", sep = ""),
                PlateID = paste(PlateID, "_mod2", sep = ""),
                NPX = sample(x = NPX, size = dplyr::n(), replace = FALSE)) |>
  dplyr::filter(!stringr::str_detect(SampleID, "CONTROL_")) |>
  dplyr::select(-Project) |>
  dplyr::mutate(Normalization = "Intensity")

## samples to use for normalization
# Bridge samples with same identifiers between npx_df1 and npx_df2
overlap_samples <- dplyr::intersect(unique(npx_df1$SampleID),
                                    unique(npx_df2$SampleID))
overlap_samples_df1_df2 <- list("DF1" = overlap_samples,
                                "DF2" = overlap_samples)
rm(overlap_samples)

# Bridge samples with different identifiers between npx_df2 and npx_df3
overlap_samples_df2_df3 <- list("DF1" = sample(x = unique(npx_df2$SampleID),
                                               size = 10,
                                               replace = FALSE),
                                "DF2" = sample(x = unique(npx_df3$SampleID),
                                               size = 10,
                                               replace = FALSE))

# Samples to use for intensity normalization between npx_df4 and the
# normalized dataset of npx_df1 and npx_df2
overlap_samples_df12_df4 <- list("DF1" = sample(x = c(unique(npx_df1$SampleID),
                                                      unique(npx_df2$SampleID)),
                                                size = 100,
                                                replace = FALSE) |>
                                   unique(),
                                 "DF2" = sample(x = unique(npx_df4$SampleID),
                                                size = 40,
                                                replace = FALSE))

# create tibble for input
norm_schema_n <- dplyr::tibble(
  order              = c(1, 2, 3, 4),
  name               = c("NPX_DF1", "NPX_DF2", "NPX_DF3", "NPX_DF4"),
  data               = list("NPX_DF1" = npx_df1,
                            "NPX_DF2" = npx_df2,
                            "NPX_DF3" = npx_df3,
                            "NPX_DF4" = npx_df4),
  samples            = list("NPX_DF1" = NA_character_,
                            "NPX_DF2" = overlap_samples_df1_df2,
                            "NPX_DF3" = overlap_samples_df2_df3,
                            "NPX_DF4" = overlap_samples_df12_df4),
  normalization_type = c(NA_character_, "Bridge", "Bridge", "Subset"),
  normalize_to       = c(NA_character_, "1", "2", "1,2")
)

olink_normalization_n(norm_schema = norm_schema_n)

OlinkAnalyze documentation built on Sept. 25, 2024, 9:07 a.m.