getSignificantSNPs {SNPassoc}

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)