isobar (version 1.18.0)

isobar-analysis: 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, ...)
"estimateRatioNumeric"(channel1,channel2,summarize.f=median, ...)
"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)
"estimateRatio"(ibspectra,noise.model,channel1,channel2, protein,peptide,...)
"estimateRatio"(ibspectra,noise.model,channel1,channel2, protein,peptide=NULL,...)
"estimateRatio"(ibspectra,noise.model,channel1,channel2,protein,peptide,...)
"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 ratiodistrIf combine=FALSE, estimateRatio returns a data.frame, with columns as described above.

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