isobar (version 1.18.0)

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

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.

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))