isobar (version 1.18.0)

Protein and peptide ratio calculation and summarization: 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

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)