Tidy PBMExperiment object

Simple helper function to convert assay format data in PBMExperiment object into a tidy tibble. If If process = TRUE, probe filtering and trimming are performed according to the probeFilter and probeTrim slots of the PBMExperiment object before passing the object to the SummarizedExperiment tidy method. If process = FALSE, the PBMExperiment is passed directly to the tidy method without any processing.

# S3 method for PBMExperiment
tidy(
  x,
  assay = SummarizedExperiment::assayNames(x)[1],
  long = FALSE,
  process = TRUE,
  ...
)

Arguments

x	a PBMExperiment object.
assay	a numeric index or string name specifying the assay to tidy. (default = `SummarizedExperiment::assayNames(x)[1]`)
long	a logical value whether to transform data to long format and include colData in output rather than default wide format with dimension similar to original PBMExperiment object. (default = FALSE)
process	a logical value whether to filter probes and trim probe sequences according to PBMExperiment rules in `probeFilter` and `probeTrim` slots. (default = TRUE)
...	other parameters for the `tidy` generic function.

Value

tibble containing values from a single PBMExperiment assay along with rowData and optionally colData.

Arguments

Value

See also