plyxp
provides efficient abstractions to the SummarizedExperiment such that using common dplyr functions feels as natural to operating on a data.frame or tibble. plyxp
was built as an alternative to the tidySummarizedExperiment
package but there may be a future in which their conflicts are reconciled. plyxp
uses data-masking from the rlang
package in order to connect dplyr functions to SummarizedExperiment slots in a manner that aims to be intuitive and avoiding ambiguity in outcomes.
Note: This package is still under active development as of Fall 2024.
installing plyxp
BiocManager::install("plyxp")
data masking SummarizedExperiment
The SummarizedExperiment
object contains three main components/“contexts” that we mask, the assays()
, rowData()
1 and colData()
.
plyxp
provides variables as-is to data within their current contexts enabling you to call S4 methods on S4 objects with dplyr
verbs. If you require access to variables outside the context, you may use pronouns made available through plyxp
to specify where to find those variables.
The .assays
, .rows
and .cols
pronouns outputs depends on the evaluating context. Users should expect that the underlying data returned from .rows
or .cols
pronouns in the assays context is a vector, replicated to match size of the assay context.
Alternatively, using a pronoun in either the rows()
or cols()
contexts will likely return a list equal in length to either nrows(rowData())
or nrows(colData())
.
Feedback
We would love to hear your feedback. Please post to Bioconductor support site or the #tidiness_in_bioc
Slack channel on community-bioc for software usage help, or post an Issue on GitHub, for software development questions.