startScore {ChIPseqR} | R Documentation

## Score potential protein binding sites

### Description

For each position in the genome this function computes a score indicating the likelihood that a protein binding site starts at that position.

### Usage

    startScore(data, b, support, background, bgCutoff, supCutoff)

### Arguments

`data` | A two column matrix with read counts. The two columns correspond to reads on the forward and reverse strand respectively.
`b` | Length of binding region.
`support` | Length of support region.
`background` | Length of background window.
`bgCutoff` | Cutoff for the change in read rates between adjacent windows (see Details).
`supCutoff` | Cutoff for the change in read rates between support regions on forward and reverse strand (see Details).

### Details

Robust estimates of read rates in background windows and support regions are obtained by limiting the difference between related estimates. Consider a forward support region of length 10 containing 20 reads. The maximum likelihood estimate for the rate parameter of the (assumed) underlying Poisson distribution is lambda_hat = 20/10 = 2. If there are 50 reads in the reverse support region a robust estimate of the rate parameter is obtained as `max(50/10, qpois(supCutoff, lambda=lambda_hat))`

### Value

Numeric vector with binding site scores.

### Note

Instead of calling this function directly use `callBindingSites`.

### Author(s)

Peter Humburg

### See Also

`callBindingSites`

[Package ChIPseqR version 1.46.0 Index]