getSignificantSNPs: Extract significant SNPs from an object of class...

In SNPassoc: SNPs-Based Whole Genome Association Studies

Extract significant SNPs from an object of class 'WGassociation'

Description

Extract significant SNPs from an object of class 'WGassociation' when genomic information is available

Usage

getSignificantSNPs(x, chromosome, model, sig = 1e-15)

Arguments

x	an object of class 'WGassociation'
chromosome	chromosome from which SNPs are extracted
model	genetic model from which SNPs are extracted
sig	statistical significance level. The default is 1e-15

Value

A list with the following components:

names	the name of SNPs
column	the columns corresponding to the SNPs in the original data frame

...

See Also

WGassociation

Examples

data(resHapMap)
# resHapMap contains the results for a log-additive genetic model

# to get the significant SNPs for chromosome 12
getSignificantSNPs(resHapMap,chromosome=12)
# to get the significant SNPs for chromosome 5
getSignificantSNPs(resHapMap,5)
# to get the significant SNPs for chromosome X at level 1e-8
getSignificantSNPs(resHapMap,5,sig=1e-8)

SNPassoc documentation built on Oct. 30, 2024, 9:26 a.m.