estimatePrimerDimer: Estimate Primer Dimers

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")

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.

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.

Examples

Run this code

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)