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 1.0.1 Index]