getArtificialDoublets {scDblFinder} | R Documentation

## getArtificialDoublets

### Description

Create expression profiles of random artificial doublets.

### Usage

    getArtificialDoublets(
      x,
      n = 3000,
      clusters = NULL,
      resamp = 0.25,
      halfSize = 0.25,
      adjustSize = 0.25,
      propRandom = 0.1,
      selMode = c("proportional", "uniform", "sqrt"),
      n.meta.cells = 2,
      meta.triplets = TRUE,
      trim.q = c(0.05, 0.95)
    )

### Arguments

`x` | A count matrix, with features as rows and cells as columns.
`n` | The approximate number of doublet to generate (default 3000).
`clusters` | The optional clusters labels to use to build cross-cluster doublets.
`resamp` | Logical; whether to resample the doublets using the poisson distribution. Alternatively, if a proportion between 0 and 1, the proportion of doublets to resample.
`halfSize` | Logical; whether to half the library size of doublets (instead of just summing up the cells). Alternatively, a number between 0 and 1 can be given, determining the proportion of the doublets for which to perform the size adjustment.
`adjustSize` | Logical; whether to adjust the size of the doublets using the ratio between each cluster's median library size. Alternatively, a number between 0 and 1 can be given, determining the proportion of the doublets for which to perform the size adjustment.
`propRandom` | The proportion of the created doublets that are fully random (default 0.1); the rest will be doublets created across clusters. Ignored if 'clusters' is NULL.
`selMode` | The cell pair selection mode for inter-cluster doublet generation, either 'uniform' (same number of doublets for each combination), 'proportional' (proportion expected from the clusters' prevalences), or 'sqrt' (roughly the square root of the expected proportion).
`n.meta.cells` | The number of meta-cell per cluster to create. If given, additional doublets will be created from cluster meta-cells. Ignored if 'clusters' is missing.
`meta.triplets` | Logical; whether to create triplets from meta cells. Ignored if 'clusters' is missing.
`trim.q` | A vector of two values between 0 and 1

### Value

A list with two elements: 'counts' (the count matrix of the artificial doublets) and 'origins' the clusters from which each artificial doublets originated (NULL if 'clusters' is not given).

### Examples

    m <- t(sapply( seq(from=0, to=5, length.out=50),
                   FUN=function(x) rpois(30,x) ) )
    doublets <- getArtificialDoublets(m, 30)

[Package scDblFinder version 1.8.0 Index]