build_gene_list_for_pathway: Build a gene list for a given pathway name

In huebschm/YAPSA: Yet Another Package for Signature Analysis

Description

Build a gene list for a given pathway name

Usage

build_gene_list_for_pathway(in_string, in_organism)

Arguments

in_string	Name or description of the pathway
in_organism	Name of the taxon to be searched in

Value

A character vector of gene names

See Also

keggLink

keggFind

extract_names_from_gene_list

Examples

 NULL
 ## Not run: 
   species <- "hsa"
   gene_lists_meta_df <- data.frame(
     name=c("BER","NHEJ","MMR"),
     explanation=c("base excision repair",
                   "non homologous end joining",
                   "mismatch repair"))
   number_of_pathways <- dim(gene_lists_meta_df)[1]
   gene_lists_list <- list()
   for (i in seq_len(number_of_pathways)) {
     temp_list <- 
       build_gene_list_for_pathway(gene_lists_meta_df$explanation[i],
                                   species)
     gene_lists_list <- c(gene_lists_list,list(temp_list))
   }
   gene_lists_list
 
## End(Not run)

huebschm/YAPSA documentation built on May 17, 2019, 9:11 p.m.