convert_ensembl_to_reactome_pw_tbl: Map ensembl gene id clone tibble to reactome pathway clone...

In GeneAccord: Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Description

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.

Usage

convert_ensembl_to_reactome_pw_tbl(mutated_gene_tbl, ensg_reactome_path_map)

Arguments

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. create_tbl_ent_clones.
ensg_reactome_path_map	A tibble with all ensembl id's and their reactome pathways. Can be loaded with data("ensg_reactome_path_map").

Details

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.

Value

The tibble containing the information of which pathway is altered in which clone.

Author(s)

Ariane L. Moore

Examples

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)

Example output

Found 2 different Ensembl gene id's in the provided alteration tibble.
0 could not be mapped to a reactome pathway.
The remaining 2 different Ensembl gene id's were mapped to 41 different reactome pathways.
There are 41 clone-pathway associations in the converted tibble.
# A tibble: 41 x 5
   file_name patient_id altered_entity                             clone1 clone2
   <chr>     <chr>      <fct>                                       <dbl>  <dbl>
 1 pat1.csv  1          Activation of NOXA and translocation to m…      0      1
 2 pat1.csv  1          Activation of PUMA and translocation to m…      0      1
 3 pat1.csv  1          Antigen processing: Ubiquitination & Prot…      1      0
 4 pat1.csv  1          Association of TriC/CCT with target prote…      0      1
 5 pat1.csv  1          Autodegradation of the E3 ubiquitin ligas…      0      1
 6 pat1.csv  1          DNA Damage/Telomere Stress Induced Senesc…      0      1
 7 pat1.csv  1          Factors involved in megakaryocyte develop…      0      1
 8 pat1.csv  1          Formation of Senescence-Associated Hetero…      0      1
 9 pat1.csv  1          G2/M Checkpoints                                0      1
10 pat1.csv  1          G2/M DNA damage checkpoint                      0      1
# … with 31 more rows
Warning message:
`as.tbl()` is deprecated as of dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 

GeneAccord documentation built on Nov. 8, 2020, 8:04 p.m.