scran_modelGeneVar Generates and stores variability data from scran::modelGeneVar in the input singleCellExperiment object

scran_modelGeneVar(inSCE, assayName)

Arguments

inSCE	a singleCellExperiment object
assayName	selected assay to compute variable features from

Value

inSCE updated singleCellExperiment object that contains variable feature metrics in rowData

Examples

data(sce_chcl, package = "scds")
sce_chcl <- scran_modelGeneVar(sce_chcl, "counts")
#> Warning: collapsing to unique 'x' values
print(head(rowData(sce_chcl)))
#> DataFrame with 6 rows and 4 columns
#>                        gene scran_modelGeneVar_mean
#>                 <character>               <numeric>
#> C12orf73           C12orf73                  0.3455
#> RNU6-1256P       RNU6-1256P                       0
#> RN7SL749P         RN7SL749P                       0
#> RNU6-157P         RNU6-157P                       0
#> SP1                     SP1                  0.0615
#> RP11-100E13.1 RP11-100E13.1                   0.004
#>               scran_modelGeneVar_totalVariance scran_modelGeneVar_bio
#>                                      <numeric>              <numeric>
#> C12orf73                     0.448353926963464    -0.0165869843482702
#> RNU6-1256P                                   0                      0
#> RN7SL749P                                    0                      0
#> RNU6-157P                                    0                      0
#> SP1                         0.0647501250625316   -0.00961413649821169
#> RP11-100E13.1              0.00398599299649809  -0.000859396801156642