Estimate Splat simulation parameters

Estimate simulation parameters for the Splat simulation from a real dataset. See the individual estimation functions for more details on how this is done.

Usage

splatEstimate(counts, params = newSplatParams())

# S3 method for class 'SingleCellExperiment'
splatEstimate(counts, params = newSplatParams())

# S3 method for class 'matrix'
splatEstimate(counts, params = newSplatParams())

Arguments

counts

either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.

params

SplatParams object to store estimated values in.

Value

SplatParams object with estimated values.

See also

splatEstMean, splatEstLib, splatEstOutlier, splatEstBCV, splatEstDropout

Examples

# Load example data
library(scuttle)
set.seed(1)
sce <- mockSCE()

params <- splatEstimate(sce)
#> NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.
params
#> A Params object of class SplatParams 
#> Parameters can be (estimable) or [not estimable], 'Default' or  'NOT DEFAULT' 
#> Secondary parameters are usually set during simulation
#> 
#> Global: 
#> (GENES)  (CELLS)   [SEED] 
#>    2000      200   787110 
#> 
#> 29 additional parameters 
#> 
#> Batches: 
#>     [BATCHES]  [BATCH CELLS]     [Location]        [Scale]       [Remove] 
#>             1            200            0.1            0.1          FALSE 
#> 
#> Mean: 
#>              (RATE)              (SHAPE) 
#> 0.00296241290380408    0.496975675076379 
#> 
#> Library size: 
#>       (LOCATION)           (SCALE)            (NORM) 
#>       357331.235  11607.2332293176              TRUE 
#> 
#> Exprs outliers: 
#> (PROBABILITY)     (Location)        (Scale) 
#>             0              4            0.5 
#> 
#> Groups: 
#>      [Groups]  [Group Probs] 
#>             1              1 
#> 
#> Diff expr: 
#> [Probability]    [Down Prob]     [Location]        [Scale] 
#>           0.1            0.5            0.1            0.4 
#> 
#> BCV: 
#>     (COMMON DISP)              (DOF) 
#> 0.752043426792851   11211.8933424086 
#> 
#> Dropout: 
#>            [Type]         (MIDPOINT)            (SHAPE) 
#>              none   2.71153553674717  -1.37209281901341 
#> 
#> Paths: 
#>         [From]         [Steps]          [Skew]    [Non-linear]  [Sigma Factor] 
#>              0             100             0.5             0.1             0.8 
#>