SeqReds: SeqReads - a container for RNAseq reads

In rnaSeqMap: rnaSeq secondary analyses

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

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

rnaSeqMap documentation built on Nov. 8, 2020, 5:50 p.m.