readSortedBam

Name of the sorted BAM file, including full path to file if
it is located outside the current working directory.

filename

a GRanges, RangesList or RangedData specifying the regions on
the reference sequence for which matches are desired. See the documentation
of the <code>Rsamtools</code> package for details.

which

Load a sorted BAM file. Optionally, only reads mapping to a specific set of
genomics coordinates are loaded. Only fields strictly necessary to run a
wavClusteR analysis are loaded.

import

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).

readSortedBam: Load a sorted BAM file

Description

Usage

Arguments

Value

References

Examples