smple_paths: Get all simple paths from KEGG pathway

In Sabor117/PathWAS: Creates predictive models of biological pathway functionality

Get all simple paths from KEGG pathway

Description

smple_paths returns a list of all simple (one-route) pathways through a larger/more complex bioogical pathway to a chosen end point.

Usage

smple_paths(
  pathway,
  gene_entrez,
  keep_routes = TRUE,
  hsapien_mart,
  saveDir = "./",
  delete_tmps = FALSE,
  cut_paths = -1
)

Arguments

pathway	character. KEGG pathway ID (e.g.: path:hsa05131).
gene_entrez	character or numeric. Entrez gene ID.
keep_routes	logical. Should the function output all simple pathways, or output a list of genes.
hsapien_mart	data frame. Data frame of gene names including at least entrezgene_id, external_gene_name.
saveDir	character. Directory for saving the KGML file downloaded from KEGG
delete_tmps	logical. After running, delete the KGML downloaded or not.
cut_paths	numeric. Cut-off for length of simple paths (default is -1 for all_smple_paths). Add threshold to reduce computing time.

Details

This function takes a pathway (possibly defined by the getpaths_frmEnds function) from KEGG and then finds all simple "routes" that lead towards a chosen end-point. Therefore it searches for every route through the pathway and searches for every gene included in those routes that lead towards the end-point. Therefore this outputs only the genes from the pathway which are associated with the end-point, and excludes genes which theoretically have no influence over the end-point.

Examples

## Find all simple routes in pathway hsa05131 (Shigellosis) leading to end point 3606 (IL18).
## Output only the genes involved in those routes (I.e. do not keep the routes themselves).

smple_paths(pathway = path:hsa05131, gene_entrez = 3606, keep_routes = FALSE)

Sabor117/PathWAS documentation built on Nov. 29, 2024, 7:44 a.m.