ContigLink-class: Class ContigLinkViewer

In jos4uke/contigLink: What the package does (short line)

Description

Class for storing descriptive statistics on the pairs of sequence that bind contigs as well as to estimate assembly quality.

Setteur method for the slot ContigLinkCount of the class ContigLinkViewer.

Setteur method for the slot InsertSizeSame of the class ContigLinkViewer.

Setteur method for the slot InsertSizeDiff of the class ContigLinkViewer.

Setteur method for the slot AssQual of the class ContigLinkViewer.

Getteur method for the slot AssQual of the class ContigLinkViewer.

Getteur method for the slot InsertSizeSame of the class ContigLinkViewer.

Getteur method for the slot InsertSizediff of the class ContigLinkViewer.

Constructor method for the class ContigLinkViewer.

Usage

## S4 method for signature 'ContigLinkViewer'
GetAssQual(object)

## S4 method for signature 'ContigLinkViewer'
GetInsertSizeSame(object)

## S4 method for signature 'ContigLinkViewer'
GetInsertSizeDiff(object)

## S4 method for signature 'ContigLinkViewer'
initialize(.Object, BamFile,
  ExperimentalInsertSize)

Arguments

BamFile	A Bam file resulting from the mapping of paired-end sequences or revers complemented mated paire on a set of contigs (assembly experiment). The Bam file has to be sorted and indexed. Sequences that do not mapped or singletons have to be filtered out.
ExperimentalInsertSize	The experimental insert size. The mean length of dna fragment that have been keeped for the sequencing experiment.
.Object	An object: see the Details section.

Details

An assembly experiment from short pairs of sequences rarely gives a uniq contig. This class aims (i) at giving some confidence indices relying to an assembly solution by computing some descriptive statistics (ii) at bringing out links between contig to propose scaffold. In this class, the information given from pairs mapping on the same contig or from pairs binding two differents contig is treated differently. Insert size estimated from sequencing pairs mapping on the same contig is used as scaffolding parameter.

This method instanciate the slots dfSame, dfDiff and ExpInsertSize. For pairs mapping on different contigs, stored in dfDiff, the Ori1 and Ori2 column are added. This columns indicates the contigs orientation so has paired-end reads are in good orientation (+ - or -> <-).

Author(s)

Delphine Charif & Joseph Tran

Delphine Charif & Joseph Tran

jos4uke/contigLink documentation built on May 19, 2019, 8:44 p.m.