Description Usage Arguments Value Author(s)

This will use either `sva`

or an SVD on the residuals
of a regression of `mat`

on `design_obs`

to estimate the
surrogate variables.

1 |

`mat` |
A numeric matrix of RNA-seq counts. The rows index the genes and the columns index the samples. |

`n_sv` |
The number of surrogate variables. |

`design_obs` |
A numeric matrix of observed covariates that are NOT to
be a part of the signal generating process. Only used in estimating the
surrogate variables (if |

`use_sva` |
A logical. Should we use surrogate variable analysis
(Leek and Storey, 2008) using |

A matrix of estimated surrogate variables. The columns index the surrogate variables and the rows index the individuals. The surrogate variables are centered and scaled to have mean 0 and variance 1.

David Gerard

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