Background subtract intensities

Source: R/backgroundSubtract.R

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.

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.