scRUVg {scMerge} | R Documentation

## RUVg function for single cell (under development)

### Description

Modified based on RUV2 from package ruv and RUVg from package RUVSeq function (see these function's documentations for full documentations and usage)

### Usage

    scRUVg(Y, ctl, k, Z = 1, eta = NULL, include.intercept = TRUE,
      fullW = NULL, svdyc = NULL)

### Arguments

`Y` | The data. A m by n matrix, where m is the number of observations and n is the number of features.
`ctl` | index vector to specify the negative controls.
`k` | The number of unwanted factors to use.
`Z` | Any additional covariates to include in the model.
`eta` | Gene-wise (as opposed to sample-wise) covariates.
`include.intercept` | Applies to both Z and eta. When Z or eta (or both) is specified (not NULL) but does not already include an intercept term, this will automatically include one. If only one of Z or eta should include an intercept, this variable should be set to FALSE, and the intercept term should be included manually where desired.
`fullW` | Can be included to speed up execution. Is returned by previous calls of scRUVg
`svdyc` | Can be included to speed up execution. For internal use; please use fullW instead.

### Value

A list consists of:

- A matrix newY, the normalised matrix,

- A matrix W, the unwanted variation matrix, and ;

- A matrix alpha, this corresponding coefficient matrix for W.

### Author(s)

Yingxin Lin, Kevin Wang

### Examples

    L = scMerge::ruvSimulate(m = 80, n = 1000, nc = 50, nCelltypes = 10)
    Y = L$Y; ctl = L$ctl
    ruvgRes = scMerge::scRUVg(Y = Y, ctl = ctl, k = 20)

[Package scMerge version 1.2.0 Index]