isobar-analysis {isobar} | R Documentation |
Calculates the relative abundance of a peptide or protein in one tag compared to another.
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, ...) ## S4 method for signature 'numeric,numeric,missing' estimateRatioNumeric(channel1,channel2,summarize.f=median, ...) ## S4 method for signature 'numeric,numeric,NoiseModel' 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) ## S4 method for signature ## 'IBSpectra,ANY,character,character,character,missing' estimateRatio(ibspectra,noise.model,channel1,channel2, protein,peptide,...) ## S4 method for signature 'IBSpectra,ANY,character,character,character,NULL' estimateRatio(ibspectra,noise.model,channel1,channel2, protein,peptide=NULL,...) ## S4 method for signature ## 'IBSpectra,ANY,character,character,missing,character' estimateRatio(ibspectra,noise.model,channel1,channel2,protein,peptide,...) ## S4 method for signature 'IBSpectra,ANY,character,character,NULL,character' estimateRatio(ibspectra,noise.model,channel1,channel2,protein=NULL,peptide,...)
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 |
quant.w.grouppeptides |
Proteins which should be quantified with group specific peptides. Normally, only reporter specific peptides are used. |
ratiodistr |
|
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 |
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 |
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 ratiodistr
If combine=FALSE, estimateRatio returns a data.frame, with columns as described above.
Florian P. Breitwieser, Jacques Colinge
ProteinGroup, IBSpectra, isobar-preprocessing, isobar-plots proteinRatios
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