Subsample genes (fast helper function for zero-inflation checks)
Source:R/subsample_genes.R
subsample_genes.RdQuickly subsample a specified number of genes from a Seurat object and
return a smaller Seurat object containing the selected features and all
original wells/samples. This is a lightweight convenience wrapper around
seqgendiff::select_counts() and is intended for creating a small
working object to run check_zeroinflation() (or similar
diagnostics) rapidly.
Arguments
- data
A Seurat object (v4 or v5) with counts in assay "RNA".
- ngene
Integer. Number of genes to keep (must be <= total genes).
- gselect
Gene-selection strategy as used by
seqgendiff::select_counts(). Defaults to"random".- seed
Integer random seed for reproducibility.
Examples
data(mini_mac)
subsample_genes(mini_mac, ngene = 50, gselect = "random", seed = 1 )
#> # A Seurat-tibble abstraction: 308 × 21
#> # Features=50 | Cells=308 | Active assay=RNA | Assays=RNA
#> .cell orig.ident nCount_RNA nFeature_RNA Plate_ID Well_ID Row Column
#> <chr> <fct> <dbl> <int> <chr> <chr> <chr> <int>
#> 1 AACAGGCAAT PMMSq033_mi… 65 29 PMMSq033 B02 B 2
#> 2 AACCAGCCAG PMMSq033_mi… 522 97 PMMSq033 C02 C 2
#> 3 AACCAGTTGA PMMSq033_mi… 415 82 PMMSq033 D02 D 2
#> 4 AACCGGCGTA PMMSq033_mi… 578 93 PMMSq033 E02 E 2
#> 5 AACCTAGTCC PMMSq033_mi… 286 72 PMMSq033 F02 F 2
#> 6 AACTCTACAC PMMSq033_mi… 515 96 PMMSq033 G02 G 2
#> 7 AACTGTGTCA PMMSq033_mi… 408 87 PMMSq033 H02 H 2
#> 8 AAGATGTCCA PMMSq033_mi… 332 78 PMMSq033 I02 I 2
#> 9 AAGCATATGG PMMSq033_mi… 498 92 PMMSq033 J02 J 2
#> 10 AAGCTCACCT PMMSq033_mi… 539 102 PMMSq033 K02 K 2
#> # ℹ 298 more rows
#> # ℹ 13 more variables: Species <chr>, Cell_type <chr>, Model_type <chr>,
#> # Time <fct>, Unit <chr>, Treatment_1 <chr>, Concentration_1 <fct>,
#> # Unit_1 <chr>, Sample_type <chr>, Project <chr>, combined_id <chr>,
#> # percent.mt <dbl>, percent.ribo <dbl>