dge_PrepKeggData: Convert DEG results tables to something Pathview can work...

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

Convert DEG results tables to something Pathview can work with

Description

Helper function to take the output table from running dge_OneFactor(), filter on an adjusted P value cutoff, and format it to something pathview can use. Also can optionally enforce sentence case for mouse gene IDs (useful when you get data from an informatics core that defaults to human-style gene names) and deduplicating by selecting the most significant fold change when duplicates are present.

Usage

dge_PrepKeggData(
  dgeRes,
  geneNames = .data$Newid,
  pval = 0.05,
  enforceSentenceCase = FALSE,
  deduplicate = FALSE
)

Arguments

dgeRes	Results table as returned by dge_OneFactor().
geneNames	Tidy Eval selection of the column in dge_OneFactor that contains the gene names. Usually Newid if you converted names to MGI symbols and GeneID if you did not.
pval	Numeric giving the P Value cutoff to use. Will keep only rows with adjusted P value less than this.
enforceSentenceCase	Boolean; should gene names be forced into sentence case (capital first letter only)?
deduplicate	Boolean; should genes be de-duplicated by keeping only the most significant instance of each one?

Value

A dataframe suitable for plotting KEGG pathways with plotKEGG().

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