olink_limma: limma analysis for Olink data

In ge11232002/OlinkR: A toolkit for Olink data analysis

Description

Given a SummarizedExperiment object, perform two groups comparison with limma package.

Usage

olink_limma(se, factorCol, contrasts, blocking = NULL)

Arguments

se	a SummarizedExperiment object.
factorCol	character(1): the metadata column in se that defines the grouping.
contrasts	character(1): a character string which can be parsed to expressions, specifying contrasts.
blocking	character(1): the metadata column in se which serves as a blocking factor.

Value

A tibble object of results from limma analysis

Author(s)

Ge Tan

Examples

npxFn <- system.file("extdata", c(
  "20200507_Inflammation_NPX_1.xlsx",
  "20200625_Inflammation_NPX_2.xlsx"
),
package = "OlinkR"
)
metaFn <- system.file("extdata", "Inflammation_Metadata.xlsx", package = "OlinkR")
se <- as_se(read_npx(npxFn, metaFn))
tb <- olink_limma(se,
  factorCol = "condition_Factor",
  contrasts = "Glucose.10mM.Vehicle - Vehicle.Vehicle",
  blocking = "Donor_Factor"
)

ge11232002/OlinkR documentation built on Jan. 17, 2022, 8:28 p.m.