Tidy all

Tidy all

tidy_all(fsce, dimnames = NULL, dims = c(1, 2), genes = NULL,
  repair = NULL)

Arguments

fsce	An object of class FunctionalSingleCellExperiment.
dimnames	vector of dimnames to retrieve. If NULL, retrieve all dimnames.
dims	vector of dimensions to retrieve
genes	vector of genes to retrieve. If NULL, retrieve all genes.
repair	vector of repair sites to retrieve. If NULL retrieve all reapir sites.

Tidying

This is a data tidier for a FunctionalSingleCellExperiment. Returns data from SingleCellExperiment in a tidy format, where variables are columns and observations are rows.

If the FunctionalSingleCellExperiment contains more than one SingleCellExperiment, data from each sce are joined using the cell_id variable name, and a new experiment column contains the name of the source sce.

See also

Other tidiers: tidy_coldata, tidy_counts, tidy_dims, tidy_logcounts

Examples

tidy_all(fsce_small, dimnames = c("UMAP"), genes = c("TP53"), repair = c("Uracil_45"))
#> harmonizing input:
#>   removing 250 sampleMap rows not in names(experiments)
#> harmonizing input:
#>   removing 250 sampleMap rows not in names(experiments)
#> # A tibble: 250 x 11
#>    experiment.x cell_id  UMAP1  UMAP2 k_cluster leiden_cluster cell_cycle
#>    <chr>        <chr>    <dbl>  <dbl> <chr>     <chr>          <chr>     
#>  1 rnaseq       TGCGGG…  1.91   0.843 2         2              S         
#>  2 rnaseq       TGGTTC… -4.01   0.781 6         4              S         
#>  3 rnaseq       CATATT…  2.50  -0.741 2         2              G2M       
#>  4 rnaseq       TCACAA…  0.891 -8.86  5         3              G1        
#>  5 rnaseq       GGAATA… -2.52   3.65  4         4              G1        
#>  6 rnaseq       CTTGGC…  0.606 -8.65  5         3              G2M       
#>  7 rnaseq       GTGAAG… -3.53   2.93  6         1              S         
#>  8 rnaseq       AGCGGT… -1.70   1.16  6         1              G1        
#>  9 rnaseq       GGATGT…  7.48   5.61  3         6              S         
#> 10 rnaseq       GTACTC… -2.30   1.47  6         1              G1        
#> # … with 240 more rows, and 4 more variables: experiment.y <chr>, TP53 <dbl>,
#> #   experiment <chr>, Uracil_45 <dbl>