find_pathway_significance {PAST}R Documentation

Find Pathway Significance

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)

[Package PAST version 1.8.0 Index]