select_phenotypes

Source: R/select_phenotypes.R

Select phenotypes to keep or exclude in the analysis

select_phenotypes(sce_object, keep = TRUE, phenotypes = NULL)

Arguments

sce_object

SingleCellExperiment object generated by format_image_to_sce
keep

TRUE if vector of phenotypes are the cells that are going to be kept, FALSE if they are to be removed
phenotypes

Vector of phenotypes of keep or exclude

Value

A SingleCellExperiment object is returned

Examples

data_subset <- select_phenotypes(SPIAT::formatted_image, keep=TRUE,
                                 phenotypes = c("AMACR",
                                 "CD3,CD8",
                                 "PDL-1"))