knockoffGenotypes.RdThis function efficiently constructs group-knockoffs of 0,1,2 variables distributed according to the fastPHASE model for unphased genotypes.
knockoffGenotypes(X, r, alpha, theta, groups = NULL, seed = 123, cluster = NULL, display_progress = FALSE)
| X | a 0,1,2 matrix of size n-by-p containing the original variables. |
|---|---|
| r | a vector of length p containing the "r" parameters estimated by fastPHASE. |
| alpha | a matrix of size p-by-K containing the "alpha" parameters estimated by fastPHASE. |
| theta | a matrix of size p-by-K containing the "theta" parameters estimated by fastPHASE. |
| groups | a vector of length p containing group memberships for each variable. Indices are assumed to be monotone increasing, starting from 1 (default: NULL). |
| seed | an integer random seed (default: 123). |
| cluster | a computing cluster object created by makeCluster (default: NULL). |
| display_progress | whether to show progress bar (default: FALSE). |
A 0,1,2 matrix of size n-by-p containing the knockoff variables.
Generate group-knockoffs of unphased genotypes according to the fastPHASE HMM. The required model parameters can be obtained through fastPHASE and loaded with loadHMM. This function is more efficient than knockoffHMM for haplotype data.
Sesia M, Katsevich E, Bates S, Candès E, Sabatti C (2019). “Multi-resolution localization of causal variants across the genome.” bioRxiv. doi: 10.1101/631390 .
Other knockoffs: knockoffDMC,
knockoffHMM,
knockoffHaplotypes
# Problem size p = 10 n = 100 # Load HMM to generate data r_file = system.file("extdata", "haplotypes_rhat.txt", package = "SNPknock") alpha_file = system.file("extdata", "haplotypes_alphahat.txt", package = "SNPknock") theta_file = system.file("extdata", "haplotypes_thetahat.txt", package = "SNPknock") char_file = system.file("extdata", "haplotypes_origchars", package = "SNPknock") hmm.data = loadHMM(r_file, alpha_file, theta_file, char_file, compact=FALSE, phased=FALSE) hmm.data$Q = hmm.data$Q[1:(p-1),,] hmm.data$pEmit = hmm.data$pEmit[1:p,,] # Sample X from this HMM X = sampleHMM(hmm.data$pInit, hmm.data$Q, hmm.data$pEmit, n=n) # Load HMM to generate knockoffs hmm = loadHMM(r_file, alpha_file, theta_file, char_file) hmm$r = hmm$r[1:p] hmm$alpha = hmm$alpha[1:p,] hmm$theta = hmm$theta[1:p,] # Generate knockoffs Xk = knockoffGenotypes(X, hmm$r, hmm$alpha, hmm$theta) # Generate group-knockoffs for groups of size 3 groups = rep(seq(p), each=3, length.out=p) Xk = knockoffGenotypes(X, hmm$r, hmm$alpha, hmm$theta, groups=groups)