assocFilter: Filter a PlGwasC object by the results of a 'plink –assoc'...

In CollapsABEL: Generalized CDH (GCDH) Analysis

Description

This is meant for reduction in computational burden. The plink --assoc does not accept covariates makes some assumptions accordingly, and thus runs faster than --linear and --logistic. SNPs that does not produce a p-value more significant than a user-set threshold will be filtered out. A new PLINK file is made and a corresponding new PlGwasC object is returned.

Usage

assocFilter(pl_gwas, plink_out_stem = NULL, p_threshold = 0.1,
  db_setup = FALSE, force = TRUE)

Arguments

pl_gwas	PlGwasC object
plink_out_stem	character. Output plink file stem (without .bed extension). The default is to add a "_filtered_RANDOM_ID" suffix to the original.
p_threshold	numeric. P-value threshold.
db_setup	logical. Whether to setup the PlGwasC object.
force	logical. Overwrite existing PLINK files.

Value

a new PlGwasC object.

Author(s)

Kaiyin Zhong, Fan Liu

Examples

## Not run: 
rbed_info = rbedInfo(bedstem = "mmp13", db_setup = FALSE)
pl_gwas = plGwas(rbed_info, 
		pheno = "mmp13.phe",
		pheno_name = "Page", 
		gwas_tag = "mmp13_page_sex_age")
runGwas(pl_gwas)
x = readGwasOut(pl_gwas, c("SNP", "P"), rmGwasOut = FALSE)
pl_gwas1 = assocFilter(pl_gwas, p_threshold = 0.001)
runGwas(pl_gwas1)
x1 = readGwasOut(pl_gwas1, c("SNP", "P"), rmGwasOut = FALSE)
y = dplyr::inner_join(x, x1, by = "SNP")
all(y$P.x == y$P.y)
all(y$P.y < 0.001)

## End(Not run)

CollapsABEL documentation built on May 1, 2019, 7:28 p.m.