mt_enrichKO: Perform enrichment analysis using KEGG annotation.

In TYMichaelsen/mmtravis: Tools for analysing (meta)transcriptomics data

Description

mt_enrichKO

Usage

mt_enrich(mmt,GeneIDs,KOs,type)

Arguments

mmt	(required) An object of class mmt.
GeneIDs	(required) Character vector with gene IDs of interest.
type	(required) String refering to which KEGG annotation scheme to use. Choose from the following: pathway - Manually curated pathway maps of known molecular interaction, reaction and relation networks. module - Manually defined functional units. reaction - Chemical reactions, mostly enzymatic reactions. reaction_class - Classes of reactions based on the chemical structure transformation patterns of substrate-product pairs.
KOs	(required) String pointing to the column in mtgene containing KO identifiers.
alternative	(optional) String specifying the direction of the test. Choose from: greater - test for enrichment in genes of interest. less - test for depletion in genes of interest. two.sided - perform a two-sided test for both in genes of interest.
show_p	(optional) numeric indicating the threshold p-value for plotting. Default: 1
size_p	(optional) numeric indicating the size of plotted p-values. Default: 1
unannotated	(optional) Should the data for unannotated genes be included in plot? Default: TRUE.

Value

A list with following:

• table - A table containing the results from the enrichment analysis.

• plot - A ggplot barplot showing reduction/enrichment of each entry in type in percent, relative to the percent found in the entire dataset.

Author(s)

Thomas Yssing Michaelsen [e-mail]

Examples

## Not run: 
# TBD.

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TYMichaelsen/mmtravis documentation built on Aug. 5, 2019, 10:48 a.m.