exportSequences

GRanges object containing individual clusters as identified
by the <a href="/link/filterClusters?package=wavClusteR&version=2.6.2" rd-options="" data-mini-rdoc="wavClusteR::filterClusters">filterClusters</a> function

clusters

A character defining the BED file name. Default to
"wavClusters.fasta"

filename

Export cluster sequences for motif search analysis (FASTA format), e.g.
using MEME-ChIP

postprocessing

The package provides an integrated pipeline for the analysis
    of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
    sequencing errors, SNPs and additional non-experimental sources by a non-
    parametric mixture model. The protein binding sites (clusters) are then resolved
    at high resolution and cluster statistics are estimated using a rigorous
    Bayesian framework. Post-processing of the results, data export for UCSC genome
    browser visualization and motif search analysis are provided. In addition, the
    package allows to integrate RNA-Seq data to estimate the False Discovery Rate
    of cluster detection. Key functions support parallel multicore computing. Note:
    while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to
    the analysis of other NGS data obtained from experimental procedures that induce
    nucleotide substitutions (e.g. BisSeq).

Federico Comoglio

wavClusteR

Sensitive and highly resolved identification of RNA-protein interaction
    sites in PAR-CLIP data

exportSequences function

GRanges object containing individual clusters as identified
by the <a href="filterClusters" rd-options="">filterClusters</a> function

exportSequences: Export cluster sequences for motif search analysis

Description

Usage

Arguments

Value

See Also