admixed {ggmix} | R Documentation |
Simulated Dataset with 1D Geography
Description
A simulated dataset to show the utility of this package
Usage
admixed
Format
An object of class list
of length 21.
Details
The code used to simulate the data is available at
https://github.com/sahirbhatnagar/ggmix/blob/master/data-raw/bnpsd-data.R.
See gen_structured_model
for more details on the output and
how the function used to simulate the data.
Value
A list with the following elements
- ytrain
simulated response vector for training set
- ytune
simulated response vector for tuning parameter selection set
- ytest
simulated response vector for test set
- xtrain
simulated design matrix for training set
- xtune
simulated design matrix for tuning parameter selection set
- xtest
simulated design matrix for testing set
- xtrain_lasso
simulated design matrix for training set for lasso model. This is the same as xtrain, but also includes the nPC principal components
- xtune_lasso
simulated design matrix for tuning parameter selection set for lasso model. This is the same as xtune, but also includes the nPC principal components
- xtest
simulated design matrix for testing set for lasso model. This is the same as xtest, but also includes the nPC principal components
- causal
character vector of the names of the causal SNPs
- beta
the vector of true regression coefficients
- kin_train
2 times the estimated kinship for the training set individuals
- kin_tune_train
The covariance matrix between the tuning set and the training set individuals
- kin_test_train
The covariance matrix between the test set and training set individuals
- Xkinship
the matrix of SNPs used to estimate the kinship matrix
- not_causal
character vector of the non-causal SNPs
- PC
the principal components for population structure adjustment
References
Ochoa, Alejandro, and John D. Storey. 2016a. "FST And Kinship for Arbitrary Population Structures I: Generalized Definitions." bioRxiv doi:10.1101/083915.
Ochoa, Alejandro, and John D. Storey. 2016b. "FST And Kinship for Arbitrary Population Structures II: Method of Moments Estimators." bioRxiv doi:10.1101/083923.
Examples
data(admixed)
str(admixed)