ibskm | R Documentation |
For GWASs, a kernel captures the pairwise similarity across a number of SNPs in each gene. Kernel projects the genotype data from original high dimensional space to a feature space. One of the more popular kernels used for genomics similarity is the identity-by-state (IBS) kernel (non- parametric function of the genotypes)
ibskm(Z)
Z |
a data matrix |
For genome-wide association study, a kernel captures the pairwise similarity across a number of SNPs in each gene. Kernel projects the genotype data from original high dimensional space to a feature space. One popular kernel used for genomics similarity is the identity-by-state (IBS) kernel, The IBS kernel does not need any assumption on the type of genetic interactions.
K |
a Gram/ kernel matrix |
Md Ashad Alam <malam@tulane.edu>
Md. Ashad Alam, Hui-Yi Lin, HOng-Wen Deng, Vince Calhour Yu-Ping Wang (2018), A kernel machine method for detecting higher order interactions in multimodal datasets: Application to schizophrenia, Journal of Neuroscience Methods, Vol. 309, 161-174.
Md Ashad Alam, Kenji Fukumizu and Yu-Ping Wang (2018), Influence Function and Robust Variant of Kernel Canonical Correlation Analysis, Neurocomputing, Vol. 304 (2018) 12-29.
M. Romanazzi (1992), Influence in canonical correlation analysis, Psychometrika vol 57(2) (1992) 237-259.
See also as gkm
, lkm
##Dummy data: X <- matrix(rnorm(200),50) ibskm(X)
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