segmentize-methods: Segmentize methods

Description Usage Arguments Details Value Methods Author(s) See Also Examples

Description

Import sequence read count data and transform it into segments.

Usage

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Arguments

counts

Integer vector with the number of reads for each position in start.

start

Integer vector with the start positions of the reads.

end

Optional integer vector with the end positions of the reads. If not supplied the values of start will be used.

chr

Optional vector with the chromosomal locations of the reads. If not supplied all reads will are assumed to be located on one chromosome.

region

Optional vector with an assignment of each read to a separate region, for example based on additional annotation. If not supplied all reads will be part of one region.

strand

Optional vector with the strand location of each read.

replicate

Optional integer vector identifying the replicate each read was obtained from, in the case of data from multiple measurements.

annotation

Optional object containing meta data passed along it the analysis. This argument does not influence the analysis.

...

Optional arguments.

pattern

Regular expression specifying the naming of the segments. The terms %1$s, %2$s, and %3$s refer to the chromosome, the strand, and the region, respectively. If not supplied the standard naming pattern %1$s_%2$s_%3$s will be used.

Details

The segmentizeCounts method takes the raw data and breaks it into segments which will be analyzed separately in the subsequent steps. Segments are defined in a way such that any has a unique combination of the input arguments chr, region, and strand. In case any of these is not supplied it is assumed that all reads belong to one chromosome, region, or strand, respectively. Usage of the region argument is beneficial if the location of potential TSS can be constrained below the level of chromosomes and strands.

Value

An object of class TssData.

Methods

Import read data and transform it into segments:

segmentizeCounts:

signature(nReads="integer", start="integer")

segmentizeCounts(counts, start, ...)

Author(s)

Maintainer: Julian Gehring <[email protected]>

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
example(physcoCounts)

## import and segmentize data
attach(physcoCounts)
x <- segmentizeCounts(counts=counts, start=start, chr=chromosome,
region=region, strand=strand)
detach(physcoCounts)

Bioconductor-mirror/TSSi documentation built on June 1, 2017, 3:20 a.m.