webgestalt_prep: Produce files for webgestalt website

In ge11232002/OlinkR: A toolkit for Olink data analysis

Description

Given a tibble object of the results returned from olink_limma function, generate the files for upload to webgestalt website.

Usage

webgestalt_prep(x, pvalue = 0.01, log2FC = 0, dir = ".")

Arguments

x	A tibble object from olink_limma function.
pvalue	The p-value to filter for significant proteins. The default is 0.01.
log2FC	The log2 fold change cut-off to filter for significant proteins. The default is 0, i.e. no filtering.
dir	The output folder. The default is current working directory.

Value

An invisible character object with exported file names.

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")
files <- webgestalt_prep(tb)
file.remove(files)

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