SeqData-class: SeqData-constructor and supported functions

In sheng-liu/SeqData: A data structure and four simple tools build upon it for sequencing data analysis

Description

The SeqData function is a constructor for constructing SeqData instances. Four supporting functions are available to conduct basic sequence analysis upon SeqData.

Usage

SeqData(bamFile=character(0),annotationFile=character(0))

Arguments

bamFie	Full path to bam file (optional).
annotationFile	Full path to annotation file (optional).

Details

This package provides a data structure and four supporting functions for sequencing data (eg.ChIPseq and RNAseq) analysis.

• SeqData an S4 data structure, contains 8 slots:

  bamFile="character",

  annotationFile="character",

  chrSize="integer",

  libSize="numeric",

  readAlignment="GAlignments",

  readCoverage="RleList",

  featureAnnotation="GRanges",

  coverageView="SimpleRleViewsList"

• Supporting fucntions Four supporting functions includes:

  viewCoverage

  countReads

  findPeaks

  annotatePeaks

Value

a SeqData object contains 8 slots with four supporting functions.

Usage

SeqData(bamFile=character(0),annotationFile=character(0))

See Also

See corresponding function documentation for details.

Examples

## seq=SeqData(bamFile="bamFileLocation",annotationFile="annotationFileLocation")

sheng-liu/SeqData documentation built on May 29, 2019, 9:22 p.m.