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

getSignificantSNPs {SNPassoc} | R Documentation

## 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(HapMap)
    # 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)

[Package SNPassoc version 1.9-2 Index]