dge_RunPathfinder: Run pathfindR analysis on output from dge_OneFactor

In NKInstinct/seqHelpers: Helper Functions for Bulk RNA-Seq Analysis

Run pathfindR analysis on output from dge_OneFactor

Description

Essentially just a wrapper around run_pathfindR(), which unfortunately also means it'll produce an HTML report and there's no way to stop it.

Usage

dge_RunPathfinder(
  dgeRes,
  geneNames = .data$Newid,
  species = "Mouse",
  reportFolder = "pathfindR_Results"
)

Arguments

dgeRes	Dataframe; the output of running dge_OneFactor()
geneNames	Column ID to choose the name of the column containing gene names (tidy evaluation).
species	Character. Currently only "Mouse" is supported, but others can be added as needed.
reportFolder	Path to folder where the pathfindR report will be saved.

Value

A dataframe showing all significantly altered KEGG pathways and the constituent genes that are up- and down-regulated.

Examples

dgeRes <- system.file("extdata", "dgeRes.Rds",
                      package = "seqHelpers") |>
    readRDS()
 ## Not run: 
    dge_RunPathfinder(dgeRes)
 
## End(Not run)

NKInstinct/seqHelpers documentation built on Aug. 20, 2022, 4:30 a.m.