isobar-analysis {isobar} | R Documentation

## IBSpectra analysis: Protein and peptide ratio calculation

### 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

[Package isobar version 1.34.0 Index]