isobar-analysis: IBSpectra analysis: Protein and peptide ratio calculation

In fbreitwieser/isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

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

Usage

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,...)

Arguments

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.

Value

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.

Author(s)

Florian P. Breitwieser, Jacques Colinge

See Also

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

Examples

  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

fbreitwieser/isobar documentation built on May 16, 2019, 12:01 p.m.