correctIntRTv1.default: correct intensity over RT for entire msexperiment

In wolski/imsbInfer: Visualization, normalization and QC of proteomics SWATH-MS data

Description

correct intensity over RT for entire msexperiment

Usage

## Default S3 method:
correctIntRTv1(obj, data, rto, plot = TRUE, k = 501,
  FUN = function(x, k = k) {     runmed(x, k = k, endrule = "constant") },
  ...)

Arguments

obj	reference data - ordered by retention time
data	to correct
rto	retention time (ordered)
plot	if TRUE create debug plot
k	smoothing with
FUN	running function - for equal median use runmed, for equal max use i.e. runFUN(x,k=300,max)
...	unused

Value

corrected data

Author(s)

Witold Wolski [e-mail]

Examples

data(SDat)
experiment = removeDecoys(SDat)
experiment = orderByRT(experiment)
cor = correctIntRTv1(experiment$Intensity[,1], experiment$Intensity[,2],experiment$RT,k=51)
cor = correctIntRTv1(experiment$Intensity[,1], experiment$Intensity[,2],experiment$RT,k=51,FUN=function(x,k=k){print(k);runFun(x,k=k,mean)})

wolski/imsbInfer documentation built on March 27, 2021, 11:39 p.m.