genepath_ListR: Create pathway gene-lists for all GTEx tissues

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

Create pathway gene-lists for all GTEx tissues

Description

genepath_ListR returns a data frame of genes for a given pathway in each tissue available in GTEx TPMs.

Usage

genepath_ListR(
  gene,
  pathway,
  tissue = NULL,
  write = TRUE,
  genelistDir = getwd(),
  hsapien_mart,
  transcriptFile,
  kgmlDir = getwd(),
  delete_tmps = FALSE,
  cut_paths = -1,
  keep_routes = TRUE
)

Arguments

gene	character or numeric (Entrez ID)
pathway	character. KEGG pathway ID (path:hsa5200).
tissue	character. Name of specific tissue for creating gene-list (must be as in GTEx TPMs file). Default is NULL which works for all tissues.
genelistDir	directory. Directory to search for and save created data frames. Default is current working directory.
hsapien_mart	data frame. Data frame of gene names including at least entrezgene_id, external_gene_name.
transcriptFile	data frame. GTEx TPMs file read as data frame.
kgmlDir	directory. Directory to search for and save KEGG KGML files. Default is current working directory.
delete_tmps	logical. Optionally delete KGMLs after creating gene list.
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 is a higher order function consisting of a run-through the creation of a gene-list for any given pathway in KEGG. The function searches in the provided directory (genelistDir) for a file with the name in the format <ENDPOINT>_<PATHWAY>_genelist.txt. If it finds one, it reads it in. If it does not find one it will create one and then save it to the specified directory.

This defaults to create a gene-list for every tissue in GTEx (including a "Complete" gene-list which incorporates every gene in the pathway with no filtering based on TPMs) for the chosen end-point + pathway combination.

This function requires several inputs. It requires the GTEx TPM files (downloaded from https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz), and it requires a BioMart file (from https://www.ensembl.org/biomart/martview/ or using package biomaRt) which includes the following columns: entrezgene_id, external_gene_name.

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