ratio-summ: Calculating and Summarizing Protein and Peptide Ratios
In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description Usage Arguments Value Author(s) See Also Examples

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.

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)

`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

'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

Florian P Breitwieser, Jacques Colinge

IBSpectra, isobar-preprocessing isobar-analysis

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)