tidy-PBMExperiment: Tidy PBMExperiment object

In pkimes/upbm: Tools for the analysis of universal protein binding microarrays

Description

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.

Usage

## S3 method for class '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.

Author(s)

Patrick Kimes

See Also

tidy-SummarizedExperiment

pkimes/upbm documentation built on Oct. 17, 2020, 9:10 a.m.