Description Usage Arguments Value Author(s) See Also Examples
Calculates the relative abundance of a peptide or protein in one tag compared to another.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | 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
|
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