relevel: Added S3 method support for
GRangesobjects containing factor columns.
encodefrom brio here.
as.DataFrameS3 method in favor of simply using S4
as.SummarizedExperimentS3 methods to support
Improved S4 method support for dplyr verbs working on
anti_join. These methods use
mergeinternally but ensure that rows are not unexpectedly reordered.
select_if. These variants keep track of row names. Internally, these functions coerce to
tbl_dfand then call the dplyr function. Return is coerced back to
DataFrame, with row names preserved.
relevel:Made S3 methods for
releveldefunct of favor of recommend S4 method usage of
droplevelsinstead. S4 method support for
droplevelsis already provided in S4Vectors (i.e.
DataFrame). Here we are improving
droplevelsfunctionality by adding additional method support for
GRanges) as well as
SummarizedExperiment, which enables automatic leveling of factors in
select*verbs to use simple base R code internally, and now methods are only defined for
DataFrameclass. This way we don’t run into any masking issues with dplyr, and we don’t need to list it as a suggested package.
Updated NAMESPACE to work with migration of some low-level functions into new acidbase package.
matchRowNameColumn: Converted function to S4 method that works on
DataFrameclass objects. Added
choicesargument, which lets the user change the column matching values, if desired.
as.SummarizedExperiment: Redefined generic to include
...in case we need to add arguments in a future update.
coerceS4ToList: Converted to S4 method approach. Now works specifically on objects that extend
Annotatedclass, such as
metadata2<-: Assign and extract metadata from either S3 or S4 objects in a consistent manner. Requires the
whichargument, similar to the approach employed in base
attr. Working example shows clearly how this differs internally between S3 (
attr) and S4 objects extending