arseq.kegg.enrich: KEGG pathway enrichment

In ajitjohnson/arseq: Automated RNA Sequencing Analysis Pipeline

Description

Performing KEGG pathway enrichment analysis on the significantly differentially expressed genes.

Usage

arseq.kegg.enrich(deg, kegg.compare = "as.group")

Arguments

deg

Differentially expressed genes dataframe returned by DESeq2 analysis

kegg.compare

Character, which comparison scheme to be used: 'paired', 'unpaired', '1ongroup', 'as.group'. 'paired' is the default, ref and samp are of equal length and one-on-one paired by the original experimental design; 'as.group', group-on-group comparison between ref and samp; 'unpaired' (used to be '1on1'), one-on-one comparison between all possible ref and samp combinations, although the original experimental design may not be one-on-one paired; '1ongroup', comparison between one samp column at a time vs the average of all ref columns.

Value

Enrichment dataframe

Examples

## Not run: 
kegg.enrich <- arseq.kegg.enrich (example_deg)

## End(Not run)

ajitjohnson/arseq documentation built on Oct. 28, 2021, 3:53 a.m.