kegg_map_enzymes: kegg_map_enzymes

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

Description

kegg_map_enzymes returns a dataset of enzymes of interested pathway.

Usage

kegg_map_enzymes(species,dataset,deg_list,
    map_number,correction_file_name,deg)

Arguments

species	A list of abbreviations of the intersested species.
dataset	The output dataset of the calculate_kegg function
deg_list	A list containing the differentially expressed genes.
map_number	A string of the interested map number.
correction_file_name	An optional filed, a string to file name, and path, of the dataset_alternate_file in case of using corrected_datasets_ids function.
deg	A logical value can be set to true in case of reurning only enzymes of differentially expressed genes, and false to return all enzymes of the intersetd pathway.

Value

A data set with three colnames, the first is the enzyme id, the second is the corresponding gene id and the third is the discription of the enzyme.

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)
enz = kegg_map_enzymes(c("adu","aip"),c,deg_list,"00061",,TRUE)

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