ratio-summ: Calculating and Summarizing Protein and Peptide Ratios

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

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)

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