Description Usage Arguments Author(s) Examples

perform fastRUVIII

1 2 3 |

`Y` |
The unnormalised SC data. A m by n matrix, where m is the number of observations and n is the number of features. |

`M` |
The replicate mapping matrix. The mapping matrix has m rows (one for each observation), and each column represents a set of replicates. The (i, j)-th entry of the mapping matrix is 1 if the i-th observation is in replicate set j, and 0 otherwise. See ruv::RUVIII for more details. |

`ctl` |
An index vector to specify the negative controls. Either a logical vector of length n or a vector of integers. |

`k` |
The number of unwanted factors to remove. This is inherited from the ruvK argument from the scMerge::scMerge function. |

`eta` |
Gene-wise (as opposed to sample-wise) covariates. See ruv::RUVIII for details. |

`rsvd_prop` |
rsvd_prop is used to control for the accuracy of the randomized SVD computation. If a lower value is used on a lower dimensional data (say < 1000 cell) will potentially yield a less accurate computed result but with a gain in speed. The default of 0.1 tends to achieve a balance between speed and accuracy. |

`include.intercept` |
When eta is specified (not NULL) but does not already include an intercept term, this will automatically include one. See ruv::RUVIII for details. |

`average` |
Average replicates after adjustment. See ruv::RUVIII for details. |

`fullalpha` |
Not used. Please ignore. See ruv::RUVIII for details. |

`return.info` |
Additional information relating to the computation of normalised matrix. We recommend setting this to true. |

`inputcheck` |
We recommend setting this to true. |

Yingxin Lin, John Ormerod, Kevin Wang

1 2 3 4 5 6 7 | ```
L = scMerge::ruvSimulate(m = 1000, n = 3000, nc = 50, nRep = 10)
Y = L$Y; M = L$M; ctl = L$ctl
improved1 = scMerge::fastRUVIII(Y = Y, M = M, ctl = ctl, k = 20, fast_svd = FALSE)
improved2 = scMerge::fastRUVIII(Y = Y, M = M, ctl = ctl, k = 20, fast_svd = TRUE, rsvd_prop = 0.1)
old = ruv::RUVIII(Y = Y, M = M, ctl = ctl, k = 20)
all.equal(improved1, old)
all.equal(improved2, old)
``` |

SydneyBioX/scMerge documentation built on Nov. 26, 2018, 10:18 a.m.

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