Description Usage Arguments Value Author(s)
View 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.
1 2 3 4 5 6 7 8 | backgroundSubtract(
pe,
assay = SummarizedExperiment::assayNames(pe)[1],
assayb = SummarizedExperiment::assayNames(pe)[2],
keepb = TRUE,
nonnegative = TRUE,
verbose = FALSE
)
|
pe |
a PBMExperiment object containing PBM intensity data. |
assay |
a numeric index or string specifying the foreground assay.
(default = |
assayb |
a numeric index or string specifying the background assay.
(default = |
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) |
PBMExperiment object with background subtracted intensities replacing the original
assay
assay values.
Patrick Kimes
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