getCutoff: Determine significance threshold for binding site scores
In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

Description Usage Arguments Value Note Author(s) References See Also

Given a vector of observed binding site scores and a desired false discovery rate, this function returns the lowest score that should be considered significant to achieve the given false discovery rate.

1	getCutoff(score, alpha = 0.05, tailCut = 0.95, adapt = FALSE, lambda, plot = TRUE, returnPval = TRUE)

`score`	Numeric vector with binding site scores.
`alpha`	Desired false discovery rate.
`tailCut`	Truncation point used to exclude outliers when fitting the null distribution.
`adapt`	Logical indicating whether an adaptive false discovery rate should be used.
`lambda`	If `adapt` is `TRUE` this is used in estimating the proportion of scores that is unrelated to binding sites.
`plot`	If this is `TRUE` (the default) a plot of the observed score distribution and estimated null distribution is generated.
`returnPval`	Indicates whether or not the corrected p-values for all scores should be returned.

A list with components

`cutoff`	A numeric vector with the score and nominal false discovery rate corresponding to the determined cutoff.
`h0`	A numeric vector with the mean and standard deviation of the estimated null distribution.
`pvalue`	If `returnPval` is `TRUE`, the p-values corresponding to the scores in `score`. Note that all missing values are removed.
`pi0`	If `adapt` is `TRUE`, the estimated proportion of scores not related to binding sites.

This function is used by callBindingSites to determine the significance threshold for peak-calling.

Peter Humburg

For the adaptive false discovery rate procedure used if adapt=TRUE see JD Storey, JE Taylor and D Siegmund. Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach. Journal of the Royal Statistical Society B, 66(1):187-205, 2004.

callBindingSites

ChIPseqR documentation built on Nov. 8, 2020, 6:49 p.m.