estimatePrimerDimer: Estimate Primer Dimers

In MassArray: Analytical Tools for MassArray Data

Description

Function to estimate level of signal due to primer dimers in a given spectrum

Usage

estimatePrimerDimer(fragments, peaks, method = c("ratio", "mann-whitney"))

Arguments

fragments	List of MassArrayFragment objects corresponding to the sample
peaks	List of MassArrayPeak objects comprising spectral data for a complete assay
method	Specifies which algorithm to use when estimating primer dimer levels (either "ratio" or "mann-whitney")

Details

Primer dimers are calculated by: 1) identifying fragments that occur within the expected primer sequence, 2) identifying which of these fragments is assayable, and 3) comparing the overall signal for primer peaks and peaks from the rest of the amplicon.

Value

Returns a list containing primer dimer ratios or significance estimates (i.e. p-values) depending on the analytical method specified ("ratio" or "mann-whitney", respectively). Returns "NA" in cases where insufficient data is present to calculate primer dimer levels.

Author(s)

Reid F. Thompson ([e-mail]), John M. Greally ([e-mail])

See Also

See Also MassArrayData

Examples

data(MassArray.example.data)
primer.data <- estimatePrimerDimer(MassArray.example.data$fragments.T, MassArray.example.data$samples[[1]]$peaks, "ratio")
mean(primer.data)
primer.data <- estimatePrimerDimer(MassArray.example.data$fragments.T, MassArray.example.data$samples[[1]]$peaks, "mann-whitney")
mean(primer.data)

MassArray documentation built on Nov. 8, 2020, 5:16 p.m.