calculate-pvalues: Calculate and Adjust Ratio and Sample p-values.

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

Functions for calculating and adjusting ratios and sample p-values. Usually, these are called by proteinRatios or peptideRatios.

Usage

  calculate.ratio.pvalue(lratio, variance, ratiodistr = NULL)
  calculate.sample.pvalue(lratio, ratiodistr)

  calculate.mult.sample.pvalue(lratio, ratiodistr, strict.pval, 
                               lower.tail, n.possible.val, n.observed.val)

  adjust.ratio.pvalue(quant.tbl, p.adjust, sign.level, globally = FALSE)

Arguments

lratio	log 10 protein or peptide ratios.
ratiodistr	Fitted ratio distribution/
variance	Variance of lratios.
strict.pval	If FALSE, missing ratios are ignored. If TRUE, missing ratios are penalized by giving them a sample.pval of 0.5.
lower.tail	lower.tail of distribution?
n.possible.val	Number of possible ratios.
n.observed.val	Number of observed ratios.
quant.tbl	Quantification table (from proteinRatios or peptideRatios).
p.adjust	p-value adjustment method (see ?p.adjust).
sign.level	Ratio significance level.
globally	Whether the p-values should be adjusted over all conditions, or individually in each condition.

Author(s)

Florian P. Breitwieser

See Also

proteinRatios,peptideRatios

Examples

  lratio <- c(-1,-1,seq(from=-1,to=1,by=.25),1,1)
  variance <- c(0,1,rep(0.1,9),0,1)
  ratiodistr.precise <- new("Norm",mean=0,sd=.25)
  ratiodistr.wide <- new("Norm",mean=0,sd=.5)

  # ratio p-value is impacted only by the variance
  # sample p-value captures whether the ratio distribution is narrow ('precise')
  #  or wide
  data.frame(lratio, variance,
             ratio.pvalue=calculate.ratio.pvalue(lratio, variance),
             sample.pvalue.precise=calculate.sample.pvalue(lratio,ratiodistr.precise),
             sample.pvalue.wide=calculate.sample.pvalue(lratio,ratiodistr.wide))

isobar documentation built on Nov. 8, 2020, 7:48 p.m.