accnet_enrichment_analysis: Enrichment analysis of accessory genome

In irycisBioinfo/PATO: Pangenome Analysis Toolkit

Enrichment analysis of accessory genome

Description

Perform a statistical test (Hypergeometric test: phyper) of the genes/proteins. It takes the cluster definition from the cluster table and compute the statistical test assuming the frequency of the gene/protein in the cluster vs the frequency of the gene/protein in the population.

Usage

accnet_enrichment_analysis(data, cluster, padj_method = "BY")

Arguments

data	An accnet object
cluster	Dataframe with two colums (Source,Cluster)
padj_method	Method adjust the p-value for multiple comparisons: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none" (see p.adjust)
max_pvalue	Maximun p-value of retrived data.

Value

Return a data.frame with the columns:

• Target: Protein

• Source: Genome

• Cluster: Cluster of genome

• perClusterFreq: Percentage (\

• ClusterFreq: Frequency 0-1 of the protein in this cluster

• ClusterGenomeSize: Number of genomes in the cluster

• perTotalFreq: Percentage (\

• TotalFreq: Frequency 0-1 of the protein in the population

• OdsRatio: Ods ration of the protein

• pvalue: p-value of the hypergeometric test (see phyper)

• padj: Adjusted p-value using p.adjust

• AccnetGenomeSize: Total number of genomes

• AccnetProteinSize: Total number of proteins

• Annot: Funtional annotation of the protein.

See Also

phyper

p.adjust

accnet

irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.