find_pathway_significance: Find Pathway Significance

In PAST: Pathway Association Study Tool (PAST)

Description

Find Pathway Significance

Usage

find_pathway_significance(
  genes,
  pathways_file,
  gene_number_cutoff = 5,
  mode,
  sample_size = 1000,
  num_cores
)

Arguments

genes	Genes from assign_SNPs_to_genes()
pathways_file	A file containing the pathway IDs, their names, and the genes in the pathway
gene_number_cutoff	A cut-off for the minimum number of genes in a pathway
mode	increasing/decreasing
sample_size	How many times to sample the effects data during random sampling
num_cores	The number of cores to use in parallelizing PAST

Value

Rugplots data

Examples

example("assign_SNPs_to_genes")
demo_pathways_file = system.file("extdata", "pathways.txt.xz",
  package = "PAST", mustWork = TRUE)
rugplots_data <- find_pathway_significance(genes, demo_pathways_file, 5,
  "increasing", 1000, 2)

PAST documentation built on Nov. 8, 2020, 8:31 p.m.