exportBindSequence: Export sequence of predicted binding sites

In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

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

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