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

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>