SNPknock

This package provides efficient algorithms to generate knockoffs for hidden Markov models, with specific support for genetic data.

Installation

To install this package, run the following command in your R console:

# For the current development version
devtools::install_github("msesia/snpknock")

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Version

Install

install.packages('SNPknock')

Monthly Downloads

185

Version

0.8.2

License

GPL-3

Maintainer

Matteo Sesia

Last Published

May 17th, 2019

Functions in SNPknock (0.8.2)

GroupGenotypes_wrapper

Wrapper for GroupGenotypes

knockoffGenotypes

Group-knockoffs of unphased genotypes

GroupHaplotypes_wrapper

Wrapper for GroupHaplotypes

knockoffDMC

Group knockoffs of discrete Markov chains

knockoffDMC_wrapper

Wrapper for DMC group knockoffs

knockoffHMM

Group knockoffs of hidden Markov models

assemble_Q

Compute the genotype transition matrices based on the fastPHASE HMM

rand_weighted

Random sampling from discrete distribution

runFastPhase

Fit an HMM to genetic data using fastPHASE

assemble_pEmit

Compute the genotype emission distributions based on the fastPHASE HMM

knockoffHMM_wrapper

Wrapper for HMM group knockoffs

knockoffHaplotypes

Group-knockoffs of phased haplotypes

assemble_pInit_phased

Compute the haplotype initial distributions based on the fastPHASE HMM

compute_Q1

Compute the haplotype transition matrices based on the fastPHASE HMM

loadEMParameters

Read the files produced by fastPHASE

loadHMM

Load HMM parameters fitted by fastPHASE

assemble_pEmit_phased

Compute the haplotype emission distributions based on the fastPHASE HMM

assemble_pInit

Compute the genotype initial distributions based on the fastPHASE HMM

sampleDMC

Sample discrete Markov chains

sampleHMM

Sample hidden Markov models

writeXtoInp

Convert genotypes X into the fastPHASE input format