CAP capture data

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Description

Data of a 5'-CAP capture experiment, after mapping the reads to the genome.

Usage

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Format

physcoCounts

Data frame with results from a 5'-CAP capture experiment, with the columns:

chromosome

Chromosome the read is mapped to.

region

Predefined region based on annotations, which can be treated independently in the analysis.

start

Start position, given as bp, of the 5' end of the read.

strand

Forward and reverse strand, given as '+' and '-', respectively.

counts

Number of reads at the respective position.

Details

The transcription data from Physcomitrella patens was mapped using the bowtie software. Then, the positions of 5' ends of each read were extracted and the number of reads at each position counted.

For further details, please see the publication.

Source

Rensing et al., 2011.

in preparation

See Also

Classes: TssData, TssNorm, TssResult

Methods: segmentizeCounts, normalizeCounts, identifyStartSites, get-methods, plot-methods, asRangedData-methods

Functions: subtract-functions

Data set: physcoCounts

Package: TSSi-package

Examples

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## load data set
data(physcoCounts)