calculate_kegg: calculate_kegg

In w-korani/keggseq: KEGG analysis and visualizing of differentially expressed genes

Description

calculate_kegg calculates hypergeometric test pvalues of kegg pathways and their adjusted_pvalue using Bonferroni method.
It takes the input of grep_datasets function or corrected_datasets_ids function as an input

Usage

calculate_kegg(dataset,deg_list)

Arguments

dataset	A output dataset of grep_datasets or corrected_datasets_ids.
deg_list	A list containing the differentially expressed genes.

Value

A data frame containg 6 colums as following:
column1: map_numbers, the map numbers of the KEGG pathway.
column2: background_gene_numbers, number of all genes included in the pathway.
column3: deg_gene_numbers, number of differentially expressed genes in the pathway.
column4: pvalue, p-value of the hypergeometric test for the pathway.
column5: adjusted_pvalue, the Bonferroni method adjustment of p-values.
column6: gene_list, a list of the differentially expressed genes included in the pathway

Examples

a <- list_species("arachis")
b <- grep_datasets(c("adu","aip"))
deg_list <- as.matrix(b[b$kegg_pathways=='00061',1])[,1]
c <- calculate_kegg(b,deg_list)

w-korani/keggseq documentation built on May 3, 2019, 7:10 p.m.