convert_ensembl_to_reactome_pw_tbl {GeneAccord} | R Documentation |
For a tibble that contains the information which ensembl gene id is mutated in which clone, map the ensembl gene id to the reactome pathways that contain this gene.
convert_ensembl_to_reactome_pw_tbl(mutated_gene_tbl, ensg_reactome_path_map)
mutated_gene_tbl |
The tibble containing the information
of which ensembl gene id is altered in which patient
and clone. Can be created with e.g.
|
ensg_reactome_path_map |
A tibble with all ensembl id's
and their reactome pathways. Can be loaded with
|
Such a tibble can be generated with e.g. the function
create_tbl_tree_collection
. If the altered entities
in the lists were the ensembl gene id's, this function
can convert the tibble into a tibble with the altered
reactome pathways. It has the columns 'file_name',
'patient_id', 'altered_entity', 'clone1', 'clone2', ... up
to the maximal number of clones (Default: until 'clone7').
If the mutated entities are ensembl gene id's, they can
be mapped with this function to the pathways from
'reactome'. The pathways are from the lowest level of hierarchy.
The tibble containing the information of which pathway is altered in which clone.
Ariane L. Moore
data("ensg_reactome_path_map") mutated_gene_tbl <- dplyr::tibble(file_name=c("pat1.csv", "pat1.csv"), patient_id=c("1","1"), altered_entity=c("ENSG00000134086", "ENSG00000141510"), clone1=c(1,0), clone2=c(0,1)) convert_ensembl_to_reactome_pw_tbl(mutated_gene_tbl, ensg_reactome_path_map)