Description Usage Arguments Details Value References See Also Examples
EpiTag
allows the selection of tag SNPs in 1 or 2 genomic regions. The selection aims at optimizing the power to detect epistasis between SNPs.
1 |
Region1 |
A nxp1 |
Region2 |
A nxp2 |
mat.MI |
An object of the class |
threshold |
Threshold applied to the Mutual Information to create the successive bins of SNP pairs. |
allelic |
A flag indicating whether data are allelic |
SMILE
is an implementation of the statistical procedure proposed in Friguet and Emily (2013). The EpiTag method is based on the computation of the "matrix" of mutual information between all pairs of SNP pairs within a single genomic region and between 2 genomic regions. Mutual information can be computed before the selection, by using the argument mat.MI
or during the selection process if mat.MI=NULL
. Based on the mutual information, EpiTag performs a greedy algorithm to iteratively select the subset of most informative SNPs to optimize power to detect epistasis.
A list containing the following components:
tagSNPs.R1 |
A |
tagSNPs.R2 |
A |
pairs.tag |
A list of pairs of SNPs selected as a tag pair. |
pairs.bins |
A list of bins of SNPs pairs. Each bin is ix2 matrix where each row is a SNP pair tagged by the corresponding tag pair in the object |
Friguet, C. and Emily, M. Selection de marqueurs pour la detection d'interactions de genes. Proceedings of 45emes Journees de Statistique, May 2013, Toulouse, France. pp.178, 2013.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | ############
## Example with simulated allelic data
############
data(RegionA)
data(RegionB)
## Computation of the mutual information and of the tag SNP selection simultaneously
res.EpiTag1 <- EpiTag(Region1=RegionA,Region2=RegionB,threshold=0.81,allelic=TRUE)
## Same results with a two steps computation of the mutual information and of the tag SNP selection
MatMI <- getMatMI(Region1=RegionA,Region2=RegionB,allelic=TRUE)
res.EpiTag2 <- EpiTag(mat.MI=MatMI,threshold=0.81,allelic=TRUE)
############
## Example with a real subset of genotypic data
############
## Loading of the genotypic data
load(system.file("extdata/Chr15_20S.Rdata", package="EpiTag"))
## Computation of the mutual information and of the tag SNP selection simultaneously
#### Can be long
res.EpiTag.real1 <- EpiTag(Region1= Chr15.20S,threshold=0.6,allelic=FALSE)
## Same results with the precomputation of the mutual information
load(system.file("extdata/MatMIChr15.Rdata", package="EpiTag")) # Loading of the precomputed array of Mutual Information
res.EpiTag.real2 <- EpiTag(mat.MI=MatMI15,threshold=0.6,allelic=FALSE)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.