isobar-analysis: IBSpectra analysis: Protein and peptide ratio calculation
In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description Usage Arguments Value Author(s) See Also Examples

Calculates the relative abundance of a peptide or protein in one tag compared to another.

estimateRatio(ibspectra, noise.model = NULL, channel1, channel2, protein, peptide, ...)
estimateRatioForPeptide(peptide, ibspectra, noise.model, channel1, channel2, combine = TRUE, ...)
estimateRatioForProtein(protein, ibspectra, noise.model, channel1, channel2, combine = TRUE, method = "isobar", specificity = REPORTERSPECIFIC, quant.w.grouppeptides = NULL, ...)

## S4 method for signature 'numeric,numeric,missing'
estimateRatioNumeric(channel1,channel2,summarize.f=median, ...)

## S4 method for signature 'numeric,numeric,NoiseModel'
estimateRatioNumeric(channel1,channel2,noise.model,ratiodistr=NULL,variance.function="maxi",
                                                            sign.level=0.05,sign.level.rat=sign.level,sign.level.sample=sign.level,
                                                            remove.outliers=TRUE,outliers.args=list(method = "iqr", outliers.coef = 1.5),
                                                            method="isobar",fc.threshold=1.3,
                                                            channel1.raw=NULL,channel2.raw=NULL,use.na=FALSE,preweights=NULL)

## S4 method for signature 
## 'IBSpectra,ANY,character,character,character,missing'
estimateRatio(ibspectra,noise.model,channel1,channel2,
                                                                              protein,peptide,...)

## S4 method for signature 'IBSpectra,ANY,character,character,character,NULL'
estimateRatio(ibspectra,noise.model,channel1,channel2,
                                                                           protein,peptide=NULL,...)

## S4 method for signature 
## 'IBSpectra,ANY,character,character,missing,character'
estimateRatio(ibspectra,noise.model,channel1,channel2,protein,peptide,...)
## S4 method for signature 'IBSpectra,ANY,character,character,NULL,character'
estimateRatio(ibspectra,noise.model,channel1,channel2,protein=NULL,peptide,...)

`ibspectra`	IBSpectra object.
`noise.model`	NoiseModel object.
`channel1`	Tag channel 1. Can either be a character denoting a 'reporter name' or a numeric vector whose value should be summarized.Ratio is calculated as channel2/channel1.
`channel2`	Tag channel 2. Can either be a character denoting a 'reporter name' or a numeric vector whose value should be summarized. Ratio is calculated as channel2/channel1.
`protein`	Protein(s) of interest. If present, channel1 and channel2 must be reporter names. Provide either proteins or peptides.
`peptide`	Peptide(s) of interest. If present, channel1 and channel2 must be reporter names. Provide either proteins or peptides.
`combine`	If true, a single ratio is returned even for multiple peptides/spectra. If false, a data.frame with a row for each peptide/protein is returned.
`specificity`	See `specificities`.
`quant.w.grouppeptides`	Proteins which should be quantified with group specific peptides. Normally, only reporter specific peptides are used.
`ratiodistr`	`distr` object of ratio distribution.
`variance.function`	Defines how the variance for ratio is calculated. 'ev' is the estimator variance and thus 1/sum(1/variances). 'wsv' is the weighted sample variance. 'maxi' method takes the maximum of the former two variances.
`sign.level`	Significiance level.
`sign.level.rat`	Signal p-value significiance level.
`sign.level.sample`	Sample p-value significiance level.
`remove.outliers`	Should outliers be removed?
`outliers.args`	Arguments for outlier removal, see OUTLIERS function (TODO).
`method`	method taken for ratio computation and selection: one of 'isobar','libra','multiq','pep','ttest' and 'compare.all'.
`fc.threshold`	When method equals fc, takes this as fold change threshold.
`summarize.f`	A method for summarizing spectrum ratios when no other information is available. For example `median` or `mean`.
`channel1.raw`	When given, noise estimation is based on channel1.raw and channel2.raw. These are the intensities of the channels before normalization.
`channel2.raw`	See channel1.raw.
`use.na`	Use NA values to calculate ratio. Experimental feature - use with caution.
`preweights`	Specifies weigths for each spectrum. Experimental feature - use with caution.

...

Passed down to estimateRatioNumeric methods.

In general, a named character vector with the following elements: - lratio: log ratio - variance - n.spectra: number of spectra available in the ratio calculation - p.value.rat: Signal p-value. NA if called w/o ratiodistr - p.value.sample: Sample p-value. NA if called w/o ratiodistr - is.significant: NA if called w/o ratiodistr

If combine=FALSE, estimateRatio returns a data.frame, with columns as described above.

Florian P. Breitwieser, Jacques Colinge

ProteinGroup, IBSpectra, isobar-preprocessing, isobar-plots proteinRatios

  data(ibspiked_set1)
  data(noise.model.hcd)
  ceru.human <- protein.g(proteinGroup(ibspiked_set1),"CERU_HUMAN")
  ceru.rat <- protein.g(proteinGroup(ibspiked_set1),"CERU_RAT")
  ceru.mouse <- protein.g(proteinGroup(ibspiked_set1),"CERU_MOUSE")
  ceru.proteins <- c(ceru.human,ceru.rat,ceru.mouse)

## Calculate ratio based on all spectra of peptides specific 
##  to CERU_HUMAN, CERU_RAT or CERU_MOUSE. Returns a named
##  numeric vector.
10^estimateRatio(ibspiked_set1,noise.model.hcd,
                 channel1="114",channel2="115",
                 protein=ceru.proteins)['lratio']

## If argument 'combine=FALSE', estimateRatio returns a data.frame 
##  with one row per protein
10^estimateRatio(ibspiked_set1,noise.model.hcd,
                 channel1="114",channel2="115",
                 protein=ceru.proteins,combine=FALSE)[,'lratio']
## spiked material channel 115 vs 114: 
##                 CERU_HUMAN (P00450): 1
##                 CERU_RAT   (P13635): 2
##                 CERU_MOUSE (Q61147): 0.5