SeqReads - a container for RNAseq reads

Description

SeqReads objects keep the reads information in the form of a list, containing one matrix of reads per experiment. Matrices of dimension n x 2 should come from a mapping to the regions defined by genome coordinates (chromosome, start, end, strand) in the SeqReads object.

The object may be filled in from the database or from list with read data. It is recommended to create one SeqReads object per gene or intergenic region. The object are used then ot create object of class NucleotideDistr

Usage

1
2
newSeqReads(chr, start, end, strand, datain=NULL, phenoData=NULL, featureData=NULL, covdesc=NULL)
newSeqReadsFromGene(g)

Arguments

chr

Chromosome

start

Start of the region on a chromosome

end

End of the region on a chromosome

strand

Genome strand: 1 or -1

datain

If supplied, it must be a list of matrices of reads start and stop

g

Ensembl identifier of a gene

phenoData
featureData
covdesc

Filename for experiment description

Value

Object of a class SeqReads

Author(s)

Michal Okoniewski, Anna Lesniewska

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