fastRUVIII {scMerge} | R Documentation

## A fast version of the ruv::RUVIII algorithm

### Description

Perform a fast version of the ruv::RUVIII algorithm for scRNA-Seq data noise estimation

### Usage

    fastRUVIII(
      Y,
      M,
      ctl,
      k = NULL,
      eta = NULL,
      svd_k = 50,
      include.intercept = TRUE,
      average = FALSE,
      BPPARAM = SerialParam(),
      BSPARAM = ExactParam(),
      fullalpha = NULL,
      return.info = FALSE,
      inputcheck = TRUE
    )

### Arguments

`Y` | The unnormalised scRNA-Seq data matrix. 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.
`svd_k` | If BSPARAM is set to `RandomParam` or `IrlbaParam` class from `BiocSingular` package, then `svd_k` will be used to used to reduce the computational cost of singular value decomposition. Default to 50.
`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.
`BPPARAM` | A `BiocParallelParam` class object from the `BiocParallel` package is used. Default is SerialParam().
`BSPARAM` | A `BiocSingularParam` class object from the `BiocSingular` package is used. Default is ExactParam().
`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.

### Value

A normalised matrix of the same dimensions as the input matrix Y.

### Author(s)

Yingxin Lin, John Ormerod, Kevin Wang

### Examples

    L = ruvSimulate(m = 200, n = 500, nc = 400, nCelltypes = 3, nBatch = 2, lambda = 0.1, sce = FALSE)
    Y = L$Y; M = L$M; ctl = L$ctl
    improved1 = scMerge::fastRUVIII(Y = Y, M = M, ctl = ctl,
    k = 20, BSPARAM = BiocSingular::ExactParam())
    improved2 = scMerge::fastRUVIII(Y = Y, M = M, ctl = ctl,
    k = 20, BSPARAM = BiocSingular::RandomParam(), svd_k = 50)
    old = ruv::RUVIII(Y = Y, M = M, ctl = ctl, k = 20)
    all.equal(improved1, old)
    all.equal(improved2, old)

[Package scMerge version 1.3.1 Index]