Description Usage Format Details Value References Examples

A simulated dataset to show the utility of this package

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An object of class `list`

of length 21.

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.

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

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.

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