transformer 0.2.0 (2019-07-19)

New methods

  • relevel: Added S3 method support for DataFrame and GRanges objects containing factor columns.

Major changes

  • Migraged atomize, decode, and encode from brio here.
  • Removed as.DataFrame S3 method in favor of simply using S4 as coercion.
  • Tightened up as.SummarizedExperiment S3 methods to support SummarizedExperiment and RangedSummarizedExperiment specifically.

Minor changes

  • Improved S3 method documentation. Use rdname tag instead of method (or legacy s3method).

transformer 0.2.1 (2019-08-05)

Minor changes

  • Improved documentation consistency, using new acidroxygen package.

transformer 0.2.2 (2019-08-08)

Minor changes

  • Reexporting dplyr left_join generic. Improved DataFrame method for left_join to keep row names, which correspond to the x object.

transformer 0.2.3 (2019-08-13)

Minor changes

  • Fix for automatic decoding of Rle columns, which will error otherwise when attempting to coerce from DataFrame to data.frame.

transformer 0.2.4 (2019-08-15)

New functions

Improved S4 method support for dplyr verbs working on DataFrame class.

  • Joins: inner_join, left_join (already defined), right_join, full_join, semi_join, and anti_join. These methods use merge internally but ensure that rows are not unexpectedly reordered.
  • Scoped variants of mutate and select: mutate_all, mutate_at, mutate_if, transmute_at, transmute_if; select_all, select_at, select_if. These variants keep track of row names. Internally, these functions coerce to tbl_df and then call the dplyr function. Return is coerced back to DataFrame, with row names preserved.

Major changes

  • relevel: Made S3 methods for relevel defunct of favor of recommend S4 method usage of droplevels instead. S4 method support for droplevels is already provided in S4Vectors (i.e. List, DataFrame). Here we are improving droplevels functionality by adding additional method support for Ranges (to support IRanges, GRanges) as well as SummarizedExperiment, which enables automatic leveling of factors in colData or rowData.

transformer 0.2.5 (2019-08-26)

Major changes

  • Renamed dplyr-like generics into camel case: innerJoin, leftJoin, rightJoin, fullJoin, semiJoin, antiJoin; mutateAll, mutateAt, mutateIf; selectIf.
  • Reworked mutate* and select* verbs to use simple base R code internally, and now methods are only defined for DataFrame class. This way we don’t run into any masking issues with dplyr, and we don’t need to list it as a suggested package.

Minor changes

  • Dropped support for select_all and select_all. These verbs don’t really make sense in the context of Bioconductor-related internal code.

transformer 0.2.6 (2019-09-03)

Minor changes

  • mutateAll: Bug fix that improves column creation with DataFrame.

transformer 0.2.7 (2019-09-09)

Minor changes

  • Made flatFiles defunct, in favor of coerceS4ToList usage.

transformer 0.2.8 (2019-10-22)

Updated NAMESPACE to work with migration of some low-level functions into new acidbase package.

Minor changes

  • matchRowNameColumn: Converted function to S4 method that works on data.frame and DataFrame class objects. Added choices argument, 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 Annotated class, such as SummarizedExperiment.

transformer 0.2.9 (2019-10-24)

New functions

  • metadata2 and metadata2<-: Assign and extract metadata from either S3 or S4 objects in a consistent manner. Requires the which argument, similar to the approach employed in base attr. Working example shows clearly how this differs internally between S3 (attr) and S4 objects extending Annotated class (metadata).

Minor changes

  • Made deprecated relevel methods (DataFrame, Ranges, SummarizedExperiment) defunct in favor of droplevels usage.

transformer 0.2.10 (2019-11-06)

Minor changes

  • Bumped Bioconductor dependencies to require 3.10 release.
  • Updated unit test code to work with newly saved objects in acidtest update.