Protein and peptide ratio calculation and summarization {isobar} | R Documentation

## Calculating and Summarizing Protein and Peptide Ratios

### Description

A set of functions to create ratios within groups and summarize them. `proteinRatios` serves as hub and calls `combn.matrix`, `combn.protein.tbl` and `summarize.ratios` successively. It can be used to calculate intra-class and inter-class ratios, to assess ratios and variability within and over cases.

### Usage

    proteinRatios(ibspectra, noise.model, reporterTagNames = NULL,
                     proteins = reporterProteins(proteinGroup(ibspectra)),
                     peptide = NULL, cl = classLabels(ibspectra),
                     combn.method = "global", combn.vs = NULL,
                     symmetry = FALSE, summarize =
                     FALSE, summarize.method = "mult.pval", min.detect =
                     NULL, strict.sample.pval = TRUE, strict.ratio.pval =
                     TRUE, orient.div = 0, sign.level = 0.05,
                     sign.level.rat = sign.level, sign.level.sample =
                     sign.level, ratiodistr = NULL, zscore.threshold =
                     NULL, variance.function = "maxi", combine = FALSE,
                     p.adjust = NULL, reverse = FALSE, cmbn = NULL,
                     before.summarize.f = NULL, ...)

    peptideRatiosNotQuant(ibspectra, ..., peptide = unique(fData(ibspectra)[!fData(ibspectra)[["use.for.quant"]], c("peptide", "modif", "site.probs")]))
    peptideRatios(ibspectra, ..., peptide = peptides(proteinGroup(ibspectra), columns = c("peptide", "modif")))

    combn.matrix(x, method = "global", cl = NULL, vs = NULL)

    combn.protein.tbl(cmbn, reverse = FALSE, ...)

    summarize.ratios(ratios, by.column = "ac", summarize.method = "mult.pval",
                     min.detect = NULL, n.combination = NULL,
                     strict.sample.pval = TRUE, strict.ratio.pval = TRUE,
                     orient.div = 0, sign.level = 0.05, sign.level.rat =
                     sign.level, sign.level.sample = sign.level,
                     variance.function = "maxi", ratiodistr = NULL)

### Arguments

`ibspectra` | IBSpectra object
`x` | for combn.matrix: reporter names. See reporterTagNames. argument of proteinRatios.
`ratios` | result of combn.protein.tbl
`by.column` | Column(s) which are the identifiers. Usually 'ac', 'peptide' or c('peptide','modif')
`cmbn` | result of combn.matrix
`before.summarize.f` | Function which is called after calculating ratios before summarizing them.
`noise.model` | NoiseModel for spectra variances
`reporterTagNames` | Reporter tags to use. By default all reporterTagNames of ibspectra object.
`proteins` | proteins for which ratios are calculated - defaults to all proteins with peptides specific to them.
`peptide` | peptides for which ratios are calculated.
`cl` | Class labels. See also ?classLabels.
`vs` | Class label or reporter tag name. When `combn.method` is "versus.class", all combinations against class `vs` are computed, when `combn.method` is "verus.channel", all combinations against channel `vs`.
`combn.method` | "global", "interclass", "intra-class", "versus.class" or "versus.channel". Defines which ratios are computed, based on class labels cl
`method` | See combn.method
`combn.vs` | vs argument for combn, if combn.method is "versus.class" or "versus.channel".
`symmetry` | If true, reports also the inverse ratio
`summarize` | If true, ratios for each protein are summarized.
`summarize.method` | "isobar", for now.
`min.detect` | How many times must a ratio for a protein be present when summarizing? When NULL, defaults to the maximum number of combinations.
`strict.sample.pval` | If true, missing ratios are penalized by giving them a sample.pval of 0.5.
`strict.ratio.pval` | If true, take all ratios into account. If false, only take ratios into account which are in the same direction as the majority of ratios
`orient.div` | Number of ratios which might go in the wrong direction.
`sign.level` | Significance level
`sign.level.rat` | Significance level on ratio p-value
`sign.level.sample` | Significance level on sample p-value
`ratiodistr` | Protein ratio distribution
`variance.function` | Variance function
`zscore.threshold` | z-score threshold to apply
`...` | Passed to estimateRatio()
`combine` | If true, a single ratio for all proteins and peptides, resp., is calculated. See `estimateRatio`.
`p.adjust` | Set to one of p.adjust.methods to adjust ratio p-values for multiple comparisions. See `p.adjust`.
`reverse` | reverse
`n.combination` | number of combinations possible

### Value

'data.frame': 11 variables:

`lratio` | log ratio
`variance` | variance
`n.spectra` | Number of spectra used for quantification
`p.value.rat` | Signal p-value (NA if ratiodistr is missing)
`p.value.sample` | Sample p-value (NA if ratiodistr is missing)
`is.significant` | Is the ratio significant? (NA if ratiodistr is missing)
`protein` | Protein quantified
`r1` | r1
`r2` | r2

### Author(s)

Florian P Breitwieser, Jacques Colinge

### See Also

IBSpectra, isobar-preprocessing isobar-analysis

### Examples

    combn.matrix(114:117,method="interclass",cl=as.character(c(1,1,2,2)))
    combn.matrix(114:117,method="interclass",cl=as.character(c(1,1,2,2)))
    combn.matrix(114:117,method="global")

    data(ibspiked_set1)
    data(noise.model.hcd)

    ceru.proteins <- c("P13635","Q61147")
    proteinRatios(ibspiked_set1,noise.model=noise.model.hcd,proteins=ceru.proteins,cl=c("T","T","C","C"),combn.method="interclass",summarize=TRUE)

[Package isobar version 1.28.1 Index]