Create a new PBMExperiment object

Source: R/PBMExperiment-constructor.R

Create a PBMExperiment object by directly specifying optional probe annotation information (probeFilter, probeTrim, probeCols), along with a based SummarizedExperiment object containing probe intensity data.

PBMExperiment(
  ...,
  pbmDesign = NULL,
  probeFilter = list(),
  probeTrim = numeric(),
  probeCols = c("Sequence", "probeID")
)

Arguments

...

an optional SummarizedExperiment containing PBM probe intensity data and corresponding annotations or parameters to be passed to the SummarizedExperiment constructor.
pbmDesign

an optional PBMDesign containing design information. If specified, probeFilter, probeTrim, and probeCols parameters will be ignored. Ignored if NULL. (default = NULL)
probeFilter

an optional named list of probe filters to be used to subset probes during data analysis steps. List names must correspond to columns in rowData. List entries must be single-parameter functions to be called on the corresponding column to return a logical vector of probes to keep (TRUE) or drop (FALSE) during analysis. (default = list())
probeTrim

an optional integer vector of length 2 specifying start and end positions in probe `Sequence' to use in analysis steps. (default = numeric())
probeCols

an optional character vector of rowData column names corresponding to probe design information. (default = c("Sequence", "probeID"))

Value

PBMExperiment object.

See also

PBMExperiment-class, SummarizedExperiment-class, gpr2PBMExperiment