Skip to contents

Replacement Methods of a ScreenR Object

Source: R/screenr-class.R
screenr_object-replace.Rd

The replacement functions of SummarizedExperiment work on ScreenR objects, with safeguards that keep the object consistent:

  • assay<- and assays<-: when the raw counts change, the normalization is removed (run normalize_data again); other assays can be added freely;

  • rowData<-: the Barcode column must equal the row names (it is added when missing); the new annotation is used by all the following analyses;

  • colData<- (and $<-): the object is checked, so for example the effective library sizes cannot be removed or made invalid while a normalization is recorded;

  • dimnames<- (rownames<-, colnames<-): the Barcode column of the rowData follows the new barcode identifiers, which must be unique.

Usage

# S4 method for class 'screenr_object,missing'
assay(x, i, withDimnames = TRUE, ...) <- value

# S4 method for class 'screenr_object,character'
assay(x, i, withDimnames = TRUE, ...) <- value

# S4 method for class 'screenr_object,numeric'
assay(x, i, withDimnames = TRUE, ...) <- value

# S4 method for class 'screenr_object,list'
assays(x, withDimnames = TRUE, ...) <- value

# S4 method for class 'screenr_object,SimpleList'
assays(x, withDimnames = TRUE, ...) <- value

# S4 method for class 'screenr_object'
rowData(x, ...) <- value

# S4 method for class 'screenr_object,DataFrame'
colData(x, ...) <- value

# S4 method for class 'screenr_object,list'
dimnames(x) <- value

Arguments

x

A ScreenR object.

i

The assay (name or index).

withDimnames, ...

Passed to the SummarizedExperiment method.

value

The new value.

Value

The modified ScreenR object.

See also

screenr_object-class

Examples

object <- get0("object", envir = asNamespace("ScreenR"))
counts <- SummarizedExperiment::assay(object, "counts")
# Changing the counts removes the normalization
SummarizedExperiment::assay(object, "counts") <- counts + 1
#> The counts have changed. The normalization has been removed: run normalize_data() again.
get_normalization(object)
#> NULL