iwNormRcosine: Raised cosine normalisation for isolation window efficiency

In msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Description

Creates a function based on a rasied cosine curve shape that will normalise any intensity values within a defined isolation window

The function that is created will output a value between 0 to 1 based on the position between the minOff and maxOff params

Usage

iwNormRcosine(minOff = -0.5, maxOff = +0.5)

Arguments

minOff	numerical; Offset to the 'left' for the precursor range. (Should be negative)
maxOff	character; Offset to the 'left' for the precursor range. (Should be positive)

Value

normalisation function for selected range

Examples

iwNormFun <- iwNormRcosine()
pm <- data.frame(mz=c(99.5, 99.9, 100, 100.1, 100.5),i=c(1000, 1000, 1000, 1000, 1000))
mzmax = 100.5
mzmin = 99.5
middle <- mzmax-(mzmax-mzmin)/2
adjustmz = pm$mz-middle

# normalise the intensities
pm$normi = pm$i*iwNormFun(adjustmz)

msPurity documentation built on Jan. 14, 2021, 2:44 a.m.