olink_ordinalRegression {OlinkAnalyze}

Function which A two-way ordinal analysis of variance can address an experimental design with two independent variables, each of which is a factor variable. The main effect of each independent variable can be tested, as well as the effect of the interaction of the two factors.

Description

Performs an ANOVA F-test for each assay (by OlinkID) in every panel using stats::Anova and Type III sum of squares. Dependent variable will be treated as ordered factor. The function handles only factor and/or covariates.

Samples that have no variable information or missing factor levels are automatically removed from the analysis (specified in a message if verbose = T). Character columns in the input dataframe are automatically converted to factors (specified in a message if verbose = T). Crossed analysis, i.e. A*B formula notation, is inferred from the variable argument in the following cases:

• c('A','B')

• c('A: B')

• c('A: B', 'B') or c('A: B', 'A')

Inference is specified in a message if verbose = T.
The formula notation of the final model is specified in a message if verbose = T.

Adjusted p-values are calculated by stats::p.adjust according to the Benjamini & Hochberg (1995) method (“fdr”). The threshold is determined by logic evaluation of Adjusted_pval < 0.05. Covariates are not included in the p-value adjustment.

Usage

olink_ordinalRegression(
  df,
  variable,
  covariates = NULL,
  return.covariates = F,
  verbose = T
)

Arguments

df

NPX or Quantified_value data frame in long format with at least protein name (Assay), OlinkID, UniProt, Panel and a factor with at least 3 levels.

variable

Single character value or character array. Variable(s) to test. If length > 1, the included variable names will be used in crossed analyses . Also takes ':'/'*' notation.

covariates

Single character value or character array. Default: NULL. Covariates to include. Takes ':'/'*' notation. Crossed analysis will not be inferred from main effects.

return.covariates

Logical. Default: False. Returns F-test results for the covariates. Note: Adjusted p-values will be NA for the covariates.

verbose

Logical. Default: True. If information about removed samples, factor conversion and final model formula is to be printed to the console.

Value

A tibble containing the ANOVA results for every protein. The tibble is arranged by ascending p-values.

Columns include:

• Assay: "character" Protein symbol

• OlinkID: "character" Olink specific ID

• UniProt: "character" UniProt ID

• Panel: "character" Name of Olink Panel

• term: "character" term in model

• statistic: "numeric" value of the statistic

• p.value: "numeric" nominal p-value

• Adjusted_pval: "numeric" adjusted p-value for the test

• Threshold: "character" if adjusted p-value is significant or not (< 0.05)

Examples

library(dplyr)

try({ # May fail if dependencies are not installed.
#Two-way Ordinal Regression with CLM.
#Results in model NPX~Treatment+Time+Treatment:Time.
   ordinalRegression_results <- olink_ordinalRegression(df = npx_data1,
                                                       variable="Treatment:Time")
})