exportBindSequence {ChIPseqR}R Documentation

Export sequence of predicted binding sites

Description

Extracts sequence of predicted binding sites from reference genome and exports them in FASTA format.

Usage

exportBindSequence(prediction, reference, bind, overlap = FALSE, file = "")

Arguments

prediction

Object of class BindScore.

reference

Reference genome sequence (as XStringSet object).

bind

Length of binding site to assume for sequence extraction. This may be missing in which case the value is derived from 'prediction'.

overlap

Logical indicating whether overlapping predictions should be allowed.

file

Name of output file.

Value

An XStringViews object containing the sequences. If a file name is provided this is returned invisibly.

Author(s)

Peter Humburg

References

Package Biostrings

See Also

XStringViews, XStringSet, BindScore


[Package ChIPseqR version 1.47.0 Index]