getCutoff {ChIPseqR} | R Documentation

## Determine significance threshold for binding site scores

### Description

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.

### Usage

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

### Arguments

`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.

### Value

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.

### Note

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

### Author(s)

Peter Humburg

### References

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.

### See Also

`callBindingSites`

[Package ChIPseqR version 1.40.0 Index]