SpectraCounteBayes: Peptide/Spectra Count Based Empirical Bayes Statistics for...

In WubingZhang/rMAUPS: Model-Based Analysis of Ubiquitin-Proteome System Based Protein Degradation.

Peptide/Spectra Count Based Empirical Bayes Statistics for Differential Expression

Description

Peptide/Spectra Count Based Empirical Bayes Statistics for Differential Expression

Usage

SpectraCounteBayes(fit, fit.method = "loess", coef_col)

Arguments

fit	an list object produced by Limma eBayes function, it should have one additional attribute $count, which stored the peptide or PSM count quantified for the gene in label-free or isobaric labelled data.
fit.method	the method used to fit variance against the number of peptides/PSM count quantified. Two available methods: "loess","nls" and "spline". default "loess"."loess" uses loess and span = 0.75, "nls"" uses a explicit formula y~a+b/x. "spline" uses smooth.spline and "generalized cross-validation" for smoothing parameter computation. For "nls", independent variable x is peptide/PSM count, response y is pooled variance (fit$sigma^2). For "loess" and "spline" method, both x and y are log transformed before applying the two methods. In most of time, "loess" is sufficient. To quickly assess the fit model, use VarianceScatterplot and Residualplot functions.
coef_col	an integer vector indicating the column(s) of fit$coefficients for which the function is to be performed. if not specified, all coefficients are used.

Details

This function adjusts the T-statistics and p-values for quantitative MS proteomics experiment according to the number of peptides/PSMs used for quantification. The method is similar in nature to intensity-based Bayes method (Maureen A. Sartor et al BMC Bioinformatics 2006).

Value

a list object with the additional attributes being: sca.t - Spectra Count Adjusted posterior t-value sca.p - Spectra Count Adjusted posterior p-value sca.dfprior - Spectra Count Adjusted prior degrees of freedom sca.priorvar- Spectra Count Adjusted estimated prior variance sca.postvar - Spectra Count Adjusted posterior variance loess.model - fitted loess model.

Author(s)

Yafeng Zhu

WubingZhang/rMAUPS documentation built on March 21, 2022, 8:48 p.m.