find_pathway_significance {PAST} | R Documentation |
Find Pathway Significance
find_pathway_significance( genes, pathways_file, gene_number_cutoff = 5, mode, sample_size = 1000, num_cores )
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 |
Rugplots data
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)