startScore: Score potential protein binding sites
In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

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

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

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

`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).

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))

Numeric vector with binding site scores.

Instead of calling this function directly use callBindingSites.

Peter Humburg

callBindingSites

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