Converts a ScreenR object created with an older version of ScreenR to the current layout. All the ScreenR functions do this automatically (with a message), so it is only needed to save the converted object, or to use it with other Bioconductor tools.
Details
Two kinds of older objects are converted:
objects created before version 1.15.8, which were not SummarizedExperiment objects;
objects created by versions 1.15.8 to 1.15.15, which stored the normalized counts as an assay and the data table as a slot.
The counts, the annotation, the groups and the sample information are
kept. The normalized counts and the data table of older objects are
not kept: those versions did not record how the counts were
normalized, and the edgeR based methods ignored the normalization, so
it cannot be recovered reliably. Run normalize_data on
the converted object (with the method used originally, "cpm" by
default). Objects of the current layout are returned unchanged.
Examples
object <- get0("object", envir = asNamespace("ScreenR"))
object <- update_screenr_object(object)
object
#> class: screenr_object
#> dim: 5320 14
#> metadata(2): screenr_layout normalization
#> assays(1): counts
#> rownames(5320): 10208 10502 ... 13876 13995
#> rowData names(5): Barcode Gene Gene_ID Sequence Library
#> colnames(14): T1 T2 ... Time4_B Time4_c
#> colData names(5): Sample Day Treatment Group EffectiveLibSize
#> normalization: cpm (effective library sizes in colData(object)$EffectiveLibSize)