PBMExperiment: Create a new PBMExperiment object

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

Description

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

Usage

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.

Author(s)

Patrick Kimes

See Also

PBMExperiment-class, SummarizedExperiment-class, gpr2PBMExperiment

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