backgroundSubtract: Background subtract intensities

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

Description

Given a PBMExperiment with foreground and background intensities, this function performs simple background subtraction and returns the same PBMExperiment object with the background intensities subtracted from the foreground intensities.

Usage

backgroundSubtract(
  pe,
  assay = SummarizedExperiment::assayNames(pe)[1],
  assayb = SummarizedExperiment::assayNames(pe)[2],
  keepb = TRUE,
  nonnegative = TRUE,
  verbose = FALSE
)

Arguments

pe	a PBMExperiment object containing PBM intensity data.
assay	a numeric index or string specifying the foreground assay. (default = SummarizedExperiment::assayNames(pe)[1])
assayb	a numeric index or string specifying the background assay. (default = SummarizedExperiment::assayNames(pe)[2])
keepb	a logical value whether to keep the background assay after subtraction. (default = TRUE)
nonnegative	a logical value whether to restrict intensities to non-negative values by setting negative values to NA. (default = TRUE)
verbose	a logical value whether to print verbose output during analysis. (default = FALSE)

Value

PBMExperiment object with background subtracted intensities replacing the original assay assay values.

Author(s)

Patrick Kimes

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