options: options

Description

The list to describe the options that are used in pathway.summaryData, pathway.rawData. It will be set by function options.default by default.

Arguments

bold

Options for testing an association:
Options for controlling data cleaning:
Options for handling huge pathways:
Options for gene-based test:
Options for pathway-based test:

describe

inspect.gene.nthe number of candidate truncation points to inspect the top genes in the pathway. The default is 10.
inspect.gene.percenta value x between 0 and 1 such that a truncation point will be defined at every x percent of the top genes. If 0 then the truncation points will be 1:inspect.gene.n. The default is 0.05.

Details

Order of removing SNPs, genes and subjects: 1. Apply the options excluded.snps and selected.snps if non-NULL. Code: RM_BY_SNP_NAMES. 2. Apply the option excluded.regions if non-NULL and if pathway.summaryData is used. Code: RM_BY_REGIONS. 2. Remove SNPs without summary statistics in summary.files. Code: NO_SUM_STAT; or remove SNPs without raw genotype data in data or geno.files. Code: NO_RAW_GENO. 3. Remove SNPs not in bim files in reference if pathway.summaryData is used. Code: NO_REF. 4. Remove SNPs with conflictive allele information in summary and reference data if pathway.summaryData is used. Code: CONF_ALLELE_INFO. 5. Remove SNPs with high missing rate. Code: SNP_MISS_RATE. 6. Remove SNPs with low MAF. Code: SNP_LOW_MAF. 7. Remove constant SNPs. Code: SNP_CONST. 8. Remove SNPs fail to pass HWE test. Code: SNP_HWE. 9. Remove highly correlated SNPs within each gene. Code: GENE_R2 or HUGE_GENE_R2. 10. Remove highly correlated SNPs within each chromosome. Code: CHR_R2, HUGE_CHR, HUGE_CHR2 or HUGE_CHR3. 11. Remove genes with high missing rate. Code: GENE_MISS_RATE. 12. Remove genes which are subsets of other genes. Code: GENE_SUBSET. Example truncation points defined by inspect.snp.n and inspect.snp.percent: Assume the number of SNPs in a gene is 100. Below are examples of the truncation points for different values of inspect.snp.n and inspect.snp.percent. Similar values are applied to inspect.gene.n and inspect.gene.percent.

rrr{ inspect.snp.n inspect.snp.percent truncation points 1 0 1 1 0.05 5 1 0.25 25 1 1 100 2 0 1, 2 2 0.05 5, 10 2 0.25 25, 50 2 1 100 3 0.2 20, 40, 60 }

Examples

Run this code

options <- options.default()
str(options)
names(options)